diff --git a/README.md b/README.md index 285ad40..6211cc9 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,8 @@ rule all: In addition, you need to create the configuration file `config.yml` and ensure it includes the appropriate configuration for `seqneut-pipeline` as described below. +To track the correct files in the created results, we suggest you copy the [./test_example/.gitignore](test_example/.gitignore) file to be the `.gitignore` for your main repo. + Finally, you need to create a `conda` environment that minimally includes the packages needed to run the pipeline, which are a recent version of [snakemake](https://snakemake.readthedocs.io/) and [pandas](https://pandas.pydata.org/). You can either create your own environment containing these, or simply build and use the one specified in [environment.yml](environment.yml) file of `seqneut-pipeline`, which is named `seqneut-pipeline`. So if you are using that environment, you can simply run the pipeline with: ``` @@ -108,16 +110,15 @@ GCATGGATCCTTTACT,A/Togo/845/2020 ``` ### viral_strain_plot_order -An optional dictionary (mapping) of viral library names (as specified in `viral_libraries`) to a CSV with a column titled "strain" that lists the strains in the order they should be plotted. -If not specified (or set to "null"), plotting is just alphabetical. -So in general, this key will look like: +A a CSV with a column named "strain" that lists the strains in the order they should be plotted. +If not specified or set to "null", then plotting is just alphabetical. +Must include all strains being used if specified. +So should look like this: ``` -viral_strain_plot_order: - pdmH1N1_lib2023_loes: data/viral_libraries/pdmH1N1_lib2023_loes_strain_order.csv - +viral_strain_plot_order: data/viral_strain_plot_order.csv ``` -The CSV files themselves will just have a column named "strain" specifying the order, such as: +The CSV file itself will just have a column named "strain" specifying the order, such as: ``` strain A/California/07/2009 @@ -328,6 +329,44 @@ Typically you might either set to 1, or "false" if you want to let the top be a Fix the bottom plateau of the neutralization curve to this value. Typicallyou might either set to 0, or "false" if you want to let the bottom be a free parameter. +### serum_titers_qc_thresholds +This key defines quality-control thresholds to apply in `serum_titers` when aggregating replicate titers for each virus for each serum. +These thresholds are designed to ensure that the serum titers reported by the pipeline are robust (sufficient replicates and sufficiently similar to the median). +It defines two variables, `min_replicates` and `max_fold_change_from_median` as follows: +``` +serum_titers_qc_thresholds: + min_replicates: 2 + max_fold_change_from_median: 3 +``` + +The `min_replicates` key defines the minimum number of replicates that must be measured for each serum, and the `max_fold_change` specifies the maximum fold-change from the serum-virus median that any replicate can have. + +### serum_titers_qc_exclusions +This key defines exclusions of replicates and QC thresholds in `serum_titers` to pass `serum_titers_qc_thresholds`. +Typically, you would set this if you have serum titers failing `serum_titer_qc_thresholds`. +It is keyed by each serum, then any viruses for that serum where we need to exclude replicates or thresholds. +Specifically, it should look like this: +``` +serum_titers_qc_exclusions: + + M099d0: + A/Bangladesh/8002/2021: + ignore_qc: true # many replicates, so ignore the extra variation around median + A/Brisbane/02/2018: + ignore_qc: true # many replicates, so ignore the extra variation around median + A/Norway/25089/2022: + replicates_to_drop: + - plate11-CGGATAAAAATGATAT # NT50 is an outlier + A/Wisconsin/588/2019: + replicates_to_drop: + - plate11-AGTCCTATCCTCAAAT # NT50 is an outlier + + +``` +Under each virus, you can set `ignore_qc: true` if you simply want to ignore any QC failures for that virus for that serum. + +If you want to exclude specific replicates, instead under the virus key set `replicates_to_drop` to be a name of the replicate for that serum-virus as named in `serum_titers`. + ## Output of the pipeline The results of running the pipeline are put in the `./results/` subdirectory of your main repo. We recommend using the `.gitignore` file in [./test_example/.gitignore] in your main repo to only track key results in your GitHub repo. @@ -348,10 +387,19 @@ The set of full created outputs are as follows (note only some will be tracked d - Outputs related to fitting the neutralization curves for each plate: - `./results/plates/{plate}/curvefits.csv`: the neutralization curve fits to each serum on each plate, including the NT50s. You should track this in repo. - `./results/plates/{plate}/curvefits.pdf`: PDF rendering the neutralization curves for the plate. You do not need to track this in the repo as a HTML version of a notebook containing the plot is tracked in `./docs/`. - - `./results/plates/{plate}/curvefits_{plate}.ipynb`: Jupyter notebook that does the curve fitting. You do not need to track this in the repo as a HTML version of the notebook is tracked in `./docs/`. + - `./results/plates/{plate}/curvefits.pickle`: pickle files with the `neutcurve.CurveFits` object for the plate. You do not need to track this in the repo as both the plots and numerical data are rendered elsewhere. - `./results/plates/{plate}/curvefits_{plate}.ipynb`: Jupyter notebook that does the curve fitting. You do not need to track this in the repo as a HTML version of the notebook is tracked in `./docs/`. - `./results/plates/{plate}/curvefits_{plate}.html`: HTML rendering of Jupyter notebook that does the curve fitting. You do not need to track this in the repo as it will be rendered in `./docs/` when the pipeline runs successfully. + - Output related to analyzing neutralization titers on a per-serum basis, aggregating across plates: + - `./results/sera/sera_by_plate.csv` summarizes which plate(s) each serum was run on. + - `./results/sera/{serum}/titers_median.csv`: titer for each virus against the serum, reported as the median across replicates. You should track this file in the repo. + - `./results/sera/{serum}/titers_per_replicate.csv`: titers for each replicate of each virus against the serum. You should track this file in the repo. + - `./results/sera/{serum}/curves.pdf`: PDF rendering of the neutralization curves for the serum. You do not need to track this in the repo as a HTML version of a notebook containing the plots is tracked in `./docs/`. + - `./results/sera/{serum}/curvefits.pickle`: pickle files with the `neutcurve.CurveFits` object for this serum, after applying QC filters. You do not need to track this in the repo as both the plots and numerical data are rendered elsewhere. + - `./results/sera/{serum}/serum_titers_{serum}.ipynb`: Jupyter notebook that aggregates titers for a serum across all plates. You do not need to track this in the repo as a HTML version of the notebook is tracked in `./docs/`. + - `./results/sera/{serum}/serum_titers_{serum}.html`: HTML rendering of the Jupyter notebook that aggregates titers for a serum across all plates. You do not need to track this in the repo as it will be rendered in `./docs/` when the pipeline runs successfully. + - `./logs/`: logs from `snakemake` rules, you may want to look at these if there are rule failures. They do not need to be tracked in the repo. ## Running pipeline to identify QC failures and fixing them @@ -359,7 +407,7 @@ If you run the pipeline via `snakemake` with the `--keep-going` flag as recommen However, if there are any QC failures that will keep it from running to completion. You will then need to manually look at the results, identify the problem (typically problematic barcodes or samples / wells), and decide how to fix the problem by using the YAML configuration file to exclude problematic barcodes / samples. -For the processing of counts to fraction infectivity, the file `./results/plates/qc_process_counts_summary.txt` will summarize the QC failures and tell you which HTML notebooks to look at for details. +For the processing of counts to fraction infectivity (`process_counts`), the file `./results/plates/qc_process_counts_summary.txt` will summarize the QC failures and tell you which HTML notebooks to look at for details. You then need to address these QC failures by doing one of the following: - Removing the offending barcodes by adding them to `barcodes_to_drop` for that plate. (If the barcode is missing in all plates, you might remove from `viral_barcodes` or `neut_standard_sets`.) @@ -368,7 +416,11 @@ You then need to address these QC failures by doing one of the following: - Adjusting the `process_counts_qc_thresholds` for that plate to be more lenient. +For the computation of serum titers against specific viruses, the file `./results/sera/qc_serum_titers_summary.txt` will summarize the QC failures and tell you which HTML notebooks to look at for details. +You will need to address these QC failures by adjusting `serum_titers_qc_exclusions` to either not worry if a serum-virus pair fails the QC filters or dropping specific serum-virus-replicate measurements. + It is expected that you may have to perform several iterations of running and fixing QC failures. +The pipeline will only run to completion when all all QC filters are passed. ## Test example and testing via GitHub Actions The [./test_example](test_example) subdirectory contains a small test example that illustrates use of the pipeline. diff --git a/environment.yml b/environment.yml index 9fd83d9..a1cc85f 100644 --- a/environment.yml +++ b/environment.yml @@ -21,4 +21,4 @@ dependencies: - ruff - pip: - dms_variants==1.4.3 - - neutcurve==0.8.0 + - neutcurve==0.10.0 diff --git a/funcs.smk b/funcs.smk index c6d950e..92183df 100644 --- a/funcs.smk +++ b/funcs.smk @@ -5,33 +5,9 @@ Designed to be included in another ``Snakefile`` that specifies the config. """ -def get_viral_strain_plot_order(viral_libs, config): - """Get the viral strain plot order.""" - viral_strain_plot_order = {viral_library: None for viral_library in viral_libs} - if "viral_strain_plot_order" in config: - viral_strain_plot_order = ( - viral_strain_plot_order | config["viral_strain_plot_order"] - ) - if set(viral_strain_plot_order) != set(viral_libs): - raise ValueError( - f"{viral_strain_plot_order.keys()=} != {viral_lib.keys()=}" - ) - for viral_library, csv in viral_strain_plot_order.items(): - viral_library_strains = sorted( - set(pd.read_csv(viral_libs[viral_library])["strain"]) - ) - if csv: - viral_order = pd.read_csv(csv)["strain"].tolist() - if len(viral_order) != len(set(viral_order)): - raise ValueError(f"duplicate strains in viral_strain_order CSV {csv}") - if set(viral_order) != set(viral_library_strains): - raise ValueError( - f"viral_strain_order does not have correct strains for {viral_library}" - ) - viral_strain_plot_order[viral_library] = viral_order - else: - viral_strain_plot_order[viral_library] = viral_library_strains - return viral_strain_plot_order +import copy +import functools +import os def process_plate(plate, plate_params): @@ -162,3 +138,15 @@ def process_plate(plate, plate_params): plate_d["samples"] = samples_df return plate_d + + +@functools.lru_cache +def sera_plates(): + """Get dict keyed by serum with values lists of plates with titers for serum.""" + csv_file = checkpoints.sera_by_plate.get().output.csv + return ( + pd.read_csv(csv_file) + .assign(plates=lambda x: x["plates"].str.split(";")) + .set_index("serum")["plates"] + .to_dict() + ) diff --git a/notebooks/curvefits.py.ipynb b/notebooks/curvefits.py.ipynb index 5d9ad30..d7c910f 100644 --- a/notebooks/curvefits.py.ipynb +++ b/notebooks/curvefits.py.ipynb @@ -16,6 +16,8 @@ "metadata": {}, "outputs": [], "source": [ + "import pickle\n", + "\n", "import neutcurve\n", "\n", "import pandas as pd" @@ -40,6 +42,7 @@ "frac_infectivity_csv = snakemake.input.frac_infectivity_csv\n", "output_csv = snakemake.output.csv\n", "output_pdf = snakemake.output.pdf\n", + "output_pickle = snakemake.output.pickle\n", "curvefit_params = snakemake.params.curvefit_params\n", "plate = snakemake.wildcards.plate" ] @@ -91,10 +94,7 @@ "print(f\"Clipping with {frac_infectivity_ceiling=}\")\n", "\n", "frac_infectivity = pd.read_csv(frac_infectivity_csv).assign(\n", - " serum_replicate=lambda x: x[\"serum\"].where(\n", - " x[\"plate_replicate\"] == plate,\n", - " x[\"serum\"] + \" (\" + x[\"plate_replicate\"].replace(plate, \"\") + \")\",\n", - " ),\n", + " replicate=lambda x: x[\"plate_replicate\"] + \"-\" + x[\"barcode\"],\n", " serum_concentration=lambda x: 1 / x[\"dilution_factor\"],\n", " frac_infectivity=lambda x: x[\"frac_infectivity\"].clip(\n", " upper=frac_infectivity_ceiling,\n", @@ -136,9 +136,9 @@ " ),\n", " conc_col=\"serum concentration\",\n", " fracinf_col=\"fraction infectivity\",\n", - " serum_col=\"serum_replicate\",\n", + " serum_col=\"serum\",\n", " virus_col=\"strain\",\n", - " replicate_col=\"barcode\",\n", + " replicate_col=\"replicate\",\n", " fixtop=curvefit_params[\"fixtop\"],\n", " fixbottom=curvefit_params[\"fixbottom\"],\n", ")" @@ -161,7 +161,7 @@ "source": [ "fig, _ = fits.plotReplicates(\n", " attempt_shared_legend=False,\n", - " legendfontsize=9,\n", + " legendfontsize=8,\n", " titlesize=10,\n", " ticksize=10,\n", " ncol=6,\n", @@ -204,32 +204,40 @@ "source": [ "fit_params = (\n", " fits.fitParams(average_only=False, no_average=True)\n", - " .rename(columns={\"serum\": \"serum_replicate\", \"replicate\": \"barcode\"})\n", " .assign(nt50=lambda x: 1 / x[\"ic50\"])\n", " .merge(\n", - " frac_infectivity[\n", - " [\"serum\", \"serum_replicate\", \"plate_replicate\"]\n", - " ].drop_duplicates(),\n", + " frac_infectivity[[\"serum\", \"replicate\"]].drop_duplicates(),\n", " validate=\"many_to_one\",\n", " )\n", - " .drop(columns=[\"ic50_str\", \"nreplicates\", \"serum_replicate\"])\n", - " .sort_values([\"serum\", \"virus\", \"plate_replicate\", \"barcode\"])\n", + " .drop(columns=[\"ic50_str\", \"nreplicates\"])\n", + " .sort_values([\"serum\", \"virus\", \"replicate\"])\n", ")\n", "\n", - "assert len(fit_params) == len(frac_infectivity.groupby([\"barcode\", \"serum_replicate\"]))\n", + "assert len(fit_params) == len(frac_infectivity.groupby([\"serum\", \"replicate\"]))\n", "\n", "print(f\"Saving to {output_csv}\")\n", "\n", "fit_params.to_csv(output_csv, index=False, float_format=\"%.4g\")" ] }, + { + "cell_type": "markdown", + "id": "79ff668d-e39c-4acb-8ef9-e6fe15a3f8f3", + "metadata": {}, + "source": [ + "Save the pickled `CurveFits` object:" + ] + }, { "cell_type": "code", "execution_count": null, - "id": "dcf7dad2-dcc4-4a5a-8b3d-9e8fa101ad1e", + "id": "c181d160-5c8f-4c8e-ae5b-32e241823ee3", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "with open(output_pickle, \"wb\") as f:\n", + " pickle.dump(fits, f)" + ] } ], "metadata": { diff --git a/notebooks/serum_titers.py.ipynb b/notebooks/serum_titers.py.ipynb new file mode 100644 index 0000000..9f47644 --- /dev/null +++ b/notebooks/serum_titers.py.ipynb @@ -0,0 +1,470 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "abe395dc-8a57-4ee8-b22e-8a1acacf1619", + "metadata": {}, + "source": [ + "# Titers for a serum\n", + "Analyze titers for a serum, aggregating replicates which may be across multiple plates." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f404cc02-6d9a-4a3a-892e-fd73f1e00b52", + "metadata": {}, + "outputs": [], + "source": [ + "import pickle\n", + "\n", + "import altair as alt\n", + "\n", + "import neutcurve\n", + "\n", + "import pandas as pd\n", + "\n", + "_ = alt.data_transformers.disable_max_rows()" + ] + }, + { + "cell_type": "markdown", + "id": "be4112bc-7d79-4b38-8e76-ec81588f40e9", + "metadata": {}, + "source": [ + "Get variables from `snakemake`:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "83425f55-9905-4cc0-b42c-440926e9a81e", + "metadata": {}, + "outputs": [], + "source": [ + "plate_fits = snakemake.input.plate_fits\n", + "pickle_fits = snakemake.input.pickles\n", + "viral_strain_plot_order = snakemake.params.viral_strain_plot_order\n", + "per_rep_titers_csv = snakemake.output.per_rep_titers\n", + "median_titers_csv = snakemake.output.median_titers\n", + "curves_pdf = snakemake.output.curves_pdf\n", + "output_pickle = snakemake.output.pickle\n", + "serum = snakemake.wildcards.serum\n", + "qc_thresholds = snakemake.params.qc_thresholds\n", + "qc_exclusions = snakemake.params.qc_exclusions\n", + "qc_failures_file = snakemake.output.qc_failures" + ] + }, + { + "cell_type": "markdown", + "id": "d3668ae9-ad6d-436e-8e7b-9a0cd3b30548", + "metadata": {}, + "source": [ + "Process the QC exclusions:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "28e5cc5f-79cf-45d0-8bad-61dbd6d9d32d", + "metadata": {}, + "outputs": [], + "source": [ + "print(f\"The QC thresholds are:\\n{qc_thresholds}\")\n", + "\n", + "# get viruses for which we are ignoring QC\n", + "viruses_ignore_qc = [\n", + " virus\n", + " for virus, d in qc_exclusions.items()\n", + " if \"ignore_qc\" in d and d[\"ignore_qc\"] is True\n", + "]\n", + "if viruses_ignore_qc:\n", + " print(\"\\nIgnoring QC for these viruses:\\n\\t\" + \"\\n\\t\".join(viruses_ignore_qc))\n", + "\n", + "# get virus replicates to drop\n", + "virus_replicates_to_drop = [\n", + " (virus, rep)\n", + " for virus, d in qc_exclusions.items()\n", + " for rep in (d[\"replicates_to_drop\"] if \"replicates_to_drop\" in d else [])\n", + "]\n", + "if virus_replicates_to_drop:\n", + " print(\n", + " \"\\nDropping these virus-replicates:\\n\\t\"\n", + " + \"\\n\\t\".join(str(tup) for tup in virus_replicates_to_drop)\n", + " )" + ] + }, + { + "cell_type": "markdown", + "id": "d96f352b-3c98-4ba9-b646-60b336b533bd", + "metadata": {}, + "source": [ + "Read all titers for this serum, dropping virus/replicates to drop:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fa38f739-e173-470a-8fc3-9e0271f4f7ad", + "metadata": {}, + "outputs": [], + "source": [ + "print(f\"Reading titers for {serum=}\")\n", + "\n", + "assert len(plate_fits)\n", + "\n", + "serum_fits = pd.concat([pd.read_csv(f) for f in plate_fits]).query(\"serum == @serum\")\n", + "\n", + "# remove virus-replicates to drop\n", + "print(f\"Read a total of {len(serum_fits)} titers\")\n", + "assert \"tup\" not in set(serum_fits.columns)\n", + "serum_fits = (\n", + " serum_fits.assign(\n", + " tup=lambda x: list(\n", + " x[[\"virus\", \"replicate\"]].itertuples(index=False, name=None)\n", + " ),\n", + " )\n", + " .query(\"tup not in @virus_replicates_to_drop\")\n", + " .drop(columns=\"tup\")\n", + ")\n", + "print(f\"Retained {len(serum_fits)} titers after dropping specified ones\")\n", + "\n", + "assert len(serum_fits), f\"no titers for {serum=}\"\n", + "assert len(serum_fits) == len(serum_fits.groupby([\"replicate\", \"virus\"]))\n", + "print(f\"Read a total of {len(serum_fits)} titers for {serum=}\")\n", + "\n", + "# get viruses in the order to plot them\n", + "viruses = sorted(serum_fits[\"virus\"].unique())\n", + "if viral_strain_plot_order is not None:\n", + " if not set(viruses).issubset(viral_strain_plot_order):\n", + " raise ValueError(\n", + " \"`viral_strain_plot_order` lacks some viruses with titers:\\n\"\n", + " + str(set(viruses) - set(viral_strain_plot_order))\n", + " )\n", + " viruses = [v for v in viral_strain_plot_order if v in viruses]\n", + "print(f\"{serum=} has titers for a total of {len(viruses)} viruses\")" + ] + }, + { + "cell_type": "markdown", + "id": "ef86e268-3840-474f-a30a-71a98f70ea86", + "metadata": {}, + "source": [ + "Get the NT50s per replicate.\n", + "Note that a lower bound in the IC50s represents and upper-bound on the NT50s:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8c10a8ec-9c57-40fe-a687-336065c61d55", + "metadata": {}, + "outputs": [], + "source": [ + "per_rep_titers = serum_fits.assign(\n", + " nt50_bound=lambda x: x[\"ic50_bound\"].map(\n", + " {\"interpolated\": \"interpolated\", \"upper\": \"lower\", \"lower\": \"upper\"}\n", + " ),\n", + ")[[\"serum\", \"replicate\", \"virus\", \"nt50\", \"nt50_bound\"]]\n", + "\n", + "assert per_rep_titers.notnull().all().all()\n", + "\n", + "print(f\"Saving {len(per_rep_titers)} per-replicate titers to {per_rep_titers_csv}\")\n", + "per_rep_titers.to_csv(per_rep_titers_csv, index=False, float_format=\"%.4g\")" + ] + }, + { + "cell_type": "markdown", + "id": "86479097-9812-43ca-b474-d304ca8a1376", + "metadata": {}, + "source": [ + "Get the median titers and the standard error of the mean. We defined the bounds (is the measurement interpolated or at a bound of the dilution series) for the median as the same as the bounds for the median measurement if there are an odd number of measurements, or if there are an even number of measurements interpolated only if all of the middle values are interpolated:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "28c53843-2979-450f-aec2-5ae80c38a83b", + "metadata": {}, + "outputs": [], + "source": [ + "def get_median_nt50_bound(s):\n", + " \"\"\"Get the bound for the median NT50.\"\"\"\n", + " s = list(s)\n", + " if len(s) % 2:\n", + " return s[len(s) // 2]\n", + " else:\n", + " bounds = s[len(s) // 2 - 1 : len(s) // 2 + 1]\n", + " assert len(bounds) == 2\n", + " if len(set(bounds)) == 1:\n", + " return bounds[0]\n", + " elif \"interpolated\" in bounds:\n", + " return [b for b in bounds if b != \"interpolated\"][0]\n", + " else:\n", + " return \"inconsistent\"\n", + "\n", + "\n", + "median_titers = (\n", + " per_rep_titers.sort_values(\"nt50\") # for getting median nt50 bound\n", + " .groupby([\"serum\", \"virus\"], as_index=False)\n", + " .aggregate(\n", + " nt50=pd.NamedAgg(\"nt50\", \"median\"),\n", + " n_replicates=pd.NamedAgg(\"replicate\", \"count\"),\n", + " nt50_stderr=pd.NamedAgg(\"nt50\", \"sem\"),\n", + " nt50_bound=pd.NamedAgg(\"nt50_bound\", get_median_nt50_bound),\n", + " )\n", + ")\n", + "\n", + "print(f\"Saving {len(median_titers)} median titers to {median_titers_csv}\")\n", + "median_titers.to_csv(median_titers_csv, index=False, float_format=\"%.4g\")" + ] + }, + { + "cell_type": "markdown", + "id": "20ef5b0d-6021-407a-92d3-083e6b7bf840", + "metadata": {}, + "source": [ + "Plot the per-replicate and median titers:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cda2f56d-ceed-43fe-9ee2-4d9365cb94e6", + "metadata": {}, + "outputs": [], + "source": [ + "virus_selection = alt.selection_point(fields=[\"virus\"], on=\"mouseover\", empty=False)\n", + "\n", + "per_rep_chart = (\n", + " alt.Chart(per_rep_titers)\n", + " .encode(\n", + " alt.X(\"virus\", sort=viruses),\n", + " alt.Y(\n", + " \"nt50\",\n", + " title=\"neutralization titer\",\n", + " scale=alt.Scale(nice=False, padding=5, type=\"log\"),\n", + " ),\n", + " alt.Shape(\"nt50_bound\", title=\"is titer bound?\"),\n", + " strokeWidth=alt.condition(virus_selection, alt.value(2), alt.value(0)),\n", + " tooltip=[\n", + " alt.Tooltip(c, format=\".3g\") if per_rep_titers[c].dtype == float else c\n", + " for c in per_rep_titers\n", + " if c != \"serum\"\n", + " ],\n", + " )\n", + " .mark_point(\n", + " size=45,\n", + " filled=True,\n", + " fillOpacity=0.5,\n", + " strokeOpacity=1,\n", + " stroke=\"black\",\n", + " color=\"#56B4E9\",\n", + " )\n", + ")\n", + "\n", + "median_chart = (\n", + " alt.Chart(median_titers)\n", + " .encode(\n", + " alt.X(\"virus\", sort=viruses),\n", + " alt.Y(\n", + " \"nt50\",\n", + " title=\"neutralization titer\",\n", + " scale=alt.Scale(nice=False, padding=5, type=\"log\"),\n", + " ),\n", + " alt.Shape(\"nt50_bound\", title=\"is titer bound?\"),\n", + " strokeWidth=alt.condition(virus_selection, alt.value(2), alt.value(0)),\n", + " tooltip=[\n", + " alt.Tooltip(c, format=\".3g\") if median_titers[c].dtype == float else c\n", + " for c in median_titers\n", + " if c != \"serum\"\n", + " ],\n", + " )\n", + " .mark_point(\n", + " color=\"#E69F00\",\n", + " size=85,\n", + " filled=True,\n", + " fillOpacity=0.9,\n", + " strokeOpacity=1,\n", + " stroke=\"black\",\n", + " )\n", + ")\n", + "\n", + "titer_chart = (\n", + " (per_rep_chart + median_chart)\n", + " .add_params(virus_selection)\n", + " .properties(\n", + " width=alt.Step(14),\n", + " height=200,\n", + " title=f\"{serum} median (orange) and per-replicate (blue) titers\",\n", + " )\n", + " .configure_axis(grid=False)\n", + ")\n", + "\n", + "titer_chart" + ] + }, + { + "cell_type": "markdown", + "id": "d3dee1b4-494e-4a3a-af39-e55200e4ef10", + "metadata": {}, + "source": [ + "Get any QC failures (ignoring any viruses for which we specified to ignore QC), and write to file:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bea8d9da-eb35-4782-9d34-57e3fbc2612b", + "metadata": {}, + "outputs": [], + "source": [ + "qc_failures = []\n", + "\n", + "insufficient_replicates = median_titers[\n", + " median_titers[\"n_replicates\"] < qc_thresholds[\"min_replicates\"]\n", + "].query(\"virus not in @viruses_ignore_qc\")\n", + "if len(insufficient_replicates):\n", + " print(f\"The following viruses fail {qc_thresholds['min_replicates']=}\")\n", + " display(insufficient_replicates)\n", + " qc_failures.append(\"min_replicates\")\n", + "else:\n", + " print(f\"All viruses pass {qc_thresholds['min_replicates']=}\")\n", + "\n", + "max_fold_change_from_median = qc_thresholds[\"max_fold_change_from_median\"]\n", + "assert max_fold_change_from_median > 1, max_fold_change_from_median\n", + "excess_fold_change_from_median = (\n", + " median_titers.rename(columns={\"nt50\": \"median_nt50\"})[[\"virus\", \"median_nt50\"]]\n", + " .merge(per_rep_titers, validate=\"one_to_many\")\n", + " .assign(\n", + " fold_change_from_median=lambda x: x[\"nt50\"] / x[\"median_nt50\"],\n", + " excess_fold_change=lambda x: (\n", + " (x[\"fold_change_from_median\"] > max_fold_change_from_median)\n", + " | (x[\"fold_change_from_median\"] < 1 / max_fold_change_from_median)\n", + " ),\n", + " )\n", + " .query(\"excess_fold_change and (virus not in @viruses_ignore_qc)\")\n", + ")\n", + "if len(excess_fold_change_from_median):\n", + " print(f\"\\nThese replicates fail {qc_thresholds['max_fold_change_from_median']=}\")\n", + " display(excess_fold_change_from_median)\n", + " qc_failures.append(\"max_fold_change_from_median\")\n", + "else:\n", + " print(f\"\\nAll viruses pass {qc_thresholds['max_fold_change_from_median']=}\")\n", + "\n", + "qc_failures = \"\\n\".join(qc_failures)\n", + "if qc_failures:\n", + " print(f\"\\nEncountered the following QC failures:\\n{qc_failures}\")\n", + "else:\n", + " print(\"\\nNo QC failures\")\n", + "print(f\"\\nLogging QC failures to {qc_failures_file}\")\n", + "with open(qc_failures_file, \"w\") as f:\n", + " f.write(qc_failures)" + ] + }, + { + "cell_type": "markdown", + "id": "0ff216ff-15af-49c5-b7c6-68533415960b", + "metadata": {}, + "source": [ + "Plot the individual neutralization curves:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "53172ad1-5fd3-4c7c-8e39-d55e331a5cfe", + "metadata": {}, + "outputs": [], + "source": [ + "# combine all the fits\n", + "fits_to_combine = []\n", + "for fname in pickle_fits:\n", + " with open(fname, \"rb\") as f:\n", + " fits_to_combine.append(pickle.load(f))\n", + "serum_curvefits = neutcurve.CurveFits.combineCurveFits(\n", + " fits_to_combine,\n", + " sera=[serum],\n", + " serum_virus_replicates_to_drop=[\n", + " (serum, virus, replicate) for (virus, replicate) in virus_replicates_to_drop\n", + " ],\n", + ")\n", + "\n", + "fig, _ = serum_curvefits.plotReplicates(\n", + " attempt_shared_legend=False,\n", + " legendfontsize=8,\n", + " ncol=4,\n", + " heightscale=1.25,\n", + " widthscale=1.25,\n", + " viruses=viruses,\n", + " subplot_titles=\"{virus}\",\n", + ")\n", + "\n", + "_ = fig.suptitle(\n", + " f\"neutralization curves for {serum}\", y=1, fontsize=18, fontweight=\"bold\"\n", + ")\n", + "\n", + "fig.tight_layout()" + ] + }, + { + "cell_type": "markdown", + "id": "b4f74eb0-2c8f-4916-9e91-aa7aa0c16ca2", + "metadata": {}, + "source": [ + "Save the curves to a file:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4da1d7c0-7100-4ca9-a14e-68e58e4d5e66", + "metadata": {}, + "outputs": [], + "source": [ + "print(f\"Saving to {curves_pdf}\")\n", + "fig.savefig(curves_pdf)" + ] + }, + { + "cell_type": "markdown", + "id": "9d8122c1-1b03-464f-af8e-5fa0fb29f50c", + "metadata": {}, + "source": [ + "Save the `CurveFits` for the serum to a pickle file:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a865011f-95a4-4852-85c6-d3e28eeaa9e6", + "metadata": {}, + "outputs": [], + "source": [ + "with open(output_pickle, \"wb\") as f:\n", + " pickle.dump(serum_curvefits, f)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/scripts/qc_serum_titers.py b/scripts/qc_serum_titers.py new file mode 100644 index 0000000..c4a19e4 --- /dev/null +++ b/scripts/qc_serum_titers.py @@ -0,0 +1,31 @@ +"""Process QC for serum titers.""" + + +import sys + + +sys.stderr = sys.stdout = log = open(snakemake.log[0], "w") + +sera = snakemake.params.sera +qc_failures = snakemake.input.qc_failures +serum_titers_htmls = snakemake.input.serum_titers_htmls + +assert len(sera) == len(qc_failures) == len(serum_titers_htmls) + +qc_summary = [] + +for serum, qc_failure, html in zip( + sera, + qc_failures, + serum_titers_htmls, +): + with open(qc_failure) as f: + failures = ["\t" + line.strip() for line in f if line.strip()] + if failures: + qc_summary.append(f"{serum} serum_titers QC failures, see {html} for details") + qc_summary += failures + else: + qc_summary.append(f"{serum} serum passed all QC") + +with open(snakemake.output.qc_summary, "w") as f: + f.write("\n".join(qc_summary)) diff --git a/scripts/sera_by_plate.py b/scripts/sera_by_plate.py new file mode 100644 index 0000000..def83e7 --- /dev/null +++ b/scripts/sera_by_plate.py @@ -0,0 +1,27 @@ +"""Get list of sera and plates for each.""" + + +import sys + +import pandas as pd + + +sys.stderr = sys.stdout = log = open(snakemake.log[0], "w") + +plates = snakemake.params.plates +curvefit_csvs = snakemake.input.csvs + +assert len(plates) == len(curvefit_csvs) == len(set(plates)) + +dfs = [] +for plate, curvefit_csv in zip(plates, curvefit_csvs): + dfs.append( + pd.read_csv(curvefit_csv)[["serum"]].drop_duplicates().assign(plate=plate) + ) + +( + pd.concat(dfs) + .groupby("serum", as_index=False) + .aggregate(plates=pd.NamedAgg("plate", lambda s: ";".join(sorted(s)))) + .to_csv(snakemake.output.csv, index=False) +) diff --git a/seqneut-pipeline.smk b/seqneut-pipeline.smk index 1ce8dcc..f213aad 100644 --- a/seqneut-pipeline.smk +++ b/seqneut-pipeline.smk @@ -5,9 +5,6 @@ Designed to be included in another ``Snakefile`` that specifies the config. """ -import copy -import os - import pandas as pd @@ -23,7 +20,15 @@ pipeline_subdir = config["seqneut-pipeline"] viral_libraries = config["viral_libraries"] -viral_strain_plot_order = get_viral_strain_plot_order(viral_libraries, config) +if ("viral_strain_plot_order" not in config) or ( + config["viral_strain_plot_order"] is None +): + viral_strain_plot_order = None +else: + viral_strain_plot_order = pd.read_csv(config["viral_strain_plot_order"])[ + "strain" + ].tolist() + assert len(viral_strain_plot_order) == len(set(viral_strain_plot_order)) neut_standard_sets = config["neut_standard_sets"] @@ -132,6 +137,7 @@ rule curvefits: output: csv="results/plates/{plate}/curvefits.csv", pdf="results/plates/{plate}/curvefits.pdf", + pickle="results/plates/{plate}/curvefits.pickle", log: notebook="results/plates/{plate}/curvefits_{plate}.ipynb", params: @@ -142,6 +148,78 @@ rule curvefits: "notebooks/curvefits.py.ipynb" +checkpoint sera_by_plate: + """Get list of all sera and plates they are on.""" + input: + csvs=expand(rules.curvefits.output.csv, plate=plates), + output: + csv="results/sera/sera_by_plate.csv", + params: + plates=list(plates), + log: + "results/logs/sera_by_plate.txt", + conda: + "environment.yml" + script: + "scripts/sera_by_plate.py" + + +rule serum_titers: + """Aggregate and analyze titers for a serum.""" + input: + plate_fits=lambda wc: [ + rules.curvefits.output.csv.format(plate=plate) + for plate in sera_plates()[wc.serum] + ], + pickles=lambda wc: [ + rules.curvefits.output.pickle.format(plate=plate) + for plate in sera_plates()[wc.serum] + ], + output: + per_rep_titers="results/sera/{serum}/titers_per_replicate.csv", + median_titers="results/sera/{serum}/titers_median.csv", + curves_pdf="results/sera/{serum}/curves.pdf", + qc_failures="results/sera/{serum}/qc_failures.txt", + pickle="results/sera/{serum}/curvefits.pickle", + params: + viral_strain_plot_order=viral_strain_plot_order, + qc_thresholds=config["serum_titers_qc_thresholds"], + qc_exclusions=lambda wc: ( + config["serum_titers_qc_exclusions"][wc.serum] + if wc.serum in config["serum_titers_qc_exclusions"] + else {} + ), + log: + notebook="results/sera/{serum}/serum_titers_{serum}.ipynb", + conda: + "environment.yml" + notebook: + "notebooks/serum_titers.py.ipynb" + + +rule qc_serum_titers: + """Check QC serum titeres from `serum_titers` rule.""" + input: + qc_failures=lambda wc: expand( + rules.serum_titers.output.qc_failures, + serum=sera_plates(), + ), + serum_titers_htmls=lambda wc: expand( + "results/sera/{serum}/serum_titers_{serum}.html", + serum=sera_plates(), + ), + output: + qc_summary="results/sera/qc_serum_titers_summary.txt", + conda: + "environment.yml" + params: + sera=lambda wc: list(sera_plates()), + log: + "results/logs/qc_serum_titers.txt", + script: + "scripts/qc_serum_titers.py" + + rule notebook_to_html: """Convert Jupyter notebook to HTML""" input: @@ -160,5 +238,7 @@ seqneut_pipeline_outputs = [ expand(rules.count_barcodes.output.counts, sample=samples), expand(rules.process_counts.output.frac_infectivity_csv, plate=plates), expand(rules.curvefits.output.csv, plate=plates), + lambda wc: expand(rules.serum_titers.output.median_titers, serum=sera_plates()), rules.qc_process_counts.output.qc_summary, + rules.qc_serum_titers.output.qc_summary, ] diff --git a/test_example/.gitignore b/test_example/.gitignore index fb904a4..f8c8c00 100644 --- a/test_example/.gitignore +++ b/test_example/.gitignore @@ -16,3 +16,11 @@ results/barcode_counts/* results/plates/*/* !results/plates/qc_process_counts_summary.txt !results/plates/*/frac_infectivity.csv +!results/plates/*/curvefits.csv + +!results/sera +results/sera/*/* +!results/sera/qc_serum_titers_summary.txt +!results/sera/sera_by_plate.csv +!results/sera/*/titers_median.csv +!results/sera/*/titers_per_replicate.csv diff --git a/test_example/config.yml b/test_example/config.yml index e62dd8c..8299c90 100644 --- a/test_example/config.yml +++ b/test_example/config.yml @@ -13,11 +13,10 @@ seqneut-pipeline: ../ viral_libraries: pdmH1N1_lib2023_loes: data/viral_libraries/pdmH1N1_lib2023_loes.csv -# If you want to plot the strains in a viral library (in `viral_libraries`) in a -# specific order, provide a CSV with column "strain" ordered in that order. If you -# omit or set to "null", will be plotted alphabetically. -viral_strain_plot_order: - pdmH1N1_lib2023_loes: data/viral_libraries/pdmH1N1_lib2023_loes_strain_order.csv +# If you want to plot the viral strains in a specific order, provide a CSV with +# column "strain" ordered in that order. If you omit or set to "null", strains +# will be plotted alphabetically. +viral_strain_plot_order: data/viral_strain_plot_order.csv # Specify the name of each set of neutralization standards and corresponding CSV # with a column "barcode" listing the barcodes @@ -61,8 +60,6 @@ illumina_barcode_parser_params: # The samples_csv must have columns "well", "serum", "dilution_factor", "replicate", and "fastq". # Other columns (eg, "notes") are allowed but are not used by the pipeline. # -# Rows beginning with '#' are considered comments and are ignored. -# # The "replicate" column indicates readings that go together as a replicate for that # serum, and only has to be unique for that serum within that plate (so you can put any # any value if the serum is only run once on that plate). @@ -122,3 +119,34 @@ plates: - C12 # low neut standard frac curvefit_params: <<: *default_curvefit_params + +# QC thresholds on per-serum virus titers. Each serum-virus titer must meet these QC +# thresholds or be specified in `serum_titers_qc_exclusions`. Otherwise titer is flagged +# as failing. +serum_titers_qc_thresholds: + min_replicates: 2 # require at least this many replicates for a serum-virus pair + max_fold_change_from_median: 3 # no replicate can have a titer more than this fold different from repicate median + +# Specify exclusions from `serum_titers_qc_thresholds. For any serum that is failing the QC, put +# a key under `serum_titer_qc_thresholds` with the name of that serum. Under that serum, in +# turn put a key with the name of the virus strain. You then have two options. You can either +# put the subkey `ignore_qc: true` to totally ignore the `serum_tiers_qc_thresholds` for that +# serum-virus pair. Alternatively, you can put `replicates_to_drop` as key followed by a +# list of the replicate names to drop (if you put all of the replicates, that virus will be +# dropped altogether for the tiers). The replicate names here are those rendered in the plots +# by the `serum_titers` notebook, which are usually of the form "{plate}-{barcode}" possibly +# with an additional plate-replicate specifier. +serum_titers_qc_exclusions: + + M099d0: + A/Bangladesh/8002/2021: + ignore_qc: true # many replicates, so ignore the extra variation around median + A/Brisbane/02/2018: + ignore_qc: true # many replicates, so ignore the extra variation around median + A/Norway/25089/2022: + replicates_to_drop: + - plate11-CGGATAAAAATGATAT # NT50 is an outlier + A/Wisconsin/588/2019: + replicates_to_drop: + - plate11-AGTCCTATCCTCAAAT # NT50 is an outlier + diff --git a/test_example/data/viral_libraries/pdmH1N1_lib2023_loes_strain_order.csv b/test_example/data/viral_strain_plot_order.csv similarity index 100% rename from test_example/data/viral_libraries/pdmH1N1_lib2023_loes_strain_order.csv rename to test_example/data/viral_strain_plot_order.csv diff --git a/test_example/results/plates/plate11/curvefits.csv b/test_example/results/plates/plate11/curvefits.csv new file mode 100644 index 0000000..c972c5b --- /dev/null +++ b/test_example/results/plates/plate11/curvefits.csv @@ -0,0 +1,331 @@ +serum,virus,replicate,ic50,ic50_bound,midpoint,slope,top,bottom,nt50 +M099d0,A/Bangladesh/2221/2021,plate11-AAGAGAAATATTCGCT,0.001789,interpolated,0.0018,15.86,0.9533,0,558.8 +M099d0,A/Bangladesh/2221/2021,plate11-GACAGCAATGCATACA,0.004322,interpolated,0.004373,29.42,0.8527,0,231.4 +M099d0,A/Bangladesh/2221/2021,plate11-GATAGAAATACCAGGA,0.001856,interpolated,0.001856,5.457,0.9997,0,538.8 +M099d0,A/Bangladesh/3210810034/2021,plate11-AACTATAGATCTAGAA,0.001711,interpolated,0.001765,4.039,0.941,0,584.3 +M099d0,A/Bangladesh/3210810034/2021,plate11-ACAAAAGTACCTCTAC,0.005397,interpolated,0.005424,21.68,0.9495,0,185.3 +M099d0,A/Bangladesh/8002/2021,plate11-AGTGTCCCTAAGAGGC,0.001778,interpolated,0.001806,5.238,0.9603,0,562.5 +M099d0,A/Bangladesh/8002/2021,plate11-GCAACGCCAAATAATT,0.002583,interpolated,0.002685,4.325,0.9227,0,387.1 +M099d0,A/Bangladesh/8002/2021,plate11-TCTGCTAAACTAAGTA,0.0011,interpolated,0.001219,2.137,0.9013,0,909.5 +M099d0,A/Bangladesh/8036/2021,plate11-ACGGGGCCCAGGTAAT,0.001797,interpolated,0.001795,4.015,1.002,0,556.4 +M099d0,A/Bangladesh/8036/2021,plate11-ATACCTCAACCTTGAA,0.003034,interpolated,0.003016,1.962,1.006,0,329.6 +M099d0,A/Bangladesh/8036/2021,plate11-CAGTTCTGCGACCAGC,0.001975,interpolated,0.00199,15.55,0.945,0,506.2 +M099d0,A/Belgium/H0017/2022,plate11-AATGAAAGTTAGCATT,0.001522,interpolated,0.001522,12.95,1,0,656.9 +M099d0,A/Belgium/H0017/2022,plate11-ATGTCCATAAAAAATA,0.001729,interpolated,0.001733,17.47,0.9766,0,578.4 +M099d0,A/Belgium/H0017/2022,plate11-GTAAAGCAAATCCATT,0.001718,interpolated,0.001731,21.87,0.9268,0,582 +M099d0,A/Belgium/H0038/2022,plate11-GATCCGTACTTTGATT,0.0006977,interpolated,0.0007407,3.171,0.9137,0,1433 +M099d0,A/Belgium/H0038/2022,plate11-GCCGGAGGGCATTTTC,0.00204,interpolated,0.002087,13.17,0.8715,0,490.2 +M099d0,A/Belgium/H0038/2022,plate11-TACCGTATAATTAAAA,0.0006168,interpolated,0.0006269,16.67,0.8812,0,1621 +M099d0,A/Brisbane/02/2018,plate11-ACGACATGATCAAACG,0.0003785,interpolated,0.0006562,1.246,0.7519,0,2642 +M099d0,A/Brisbane/02/2018,plate11-ATCCGATTTAAAGGCA,0.001339,interpolated,0.00142,2.297,0.937,0,746.6 +M099d0,A/Brisbane/02/2018,plate11-TAATAAGCCAGCAAGA,0.001136,interpolated,0.001164,3.749,0.9554,0,880.7 +M099d0,A/Brisbane/02/2018,plate11-TTGGGCACTAAATTAA,0.001704,interpolated,0.00171,18.92,0.966,0,586.9 +M099d0,A/Brisbane/48/2022,plate11-CCCTATGCTGCGTATT,0.002247,interpolated,0.002392,2.078,0.939,0,445.1 +M099d0,A/Brisbane/48/2022,plate11-GAGCTCTAAAGCAACA,0.004774,interpolated,0.004804,23.33,0.9308,0,209.5 +M099d0,A/Brisbane/48/2022,plate11-TTATGATCTAAACAGA,0.001808,interpolated,0.001823,24.48,0.9134,0,553 +M099d0,A/California/07/2009,plate11-CATGTGAATTCGCCCA,0.001631,interpolated,0.001634,19.36,0.9813,0,613.2 +M099d0,A/California/07/2009,plate11-CCTTTCTCAAAACATA,0.001681,interpolated,0.001694,21.59,0.9201,0,595 +M099d0,A/California/07/2009,plate11-CGCCTAATGTTAATAA,0.001607,interpolated,0.001613,17.96,0.9693,0,622.2 +M099d0,A/California/07/2009,plate11-GACACAGAACCCATGC,0.001154,interpolated,0.001154,5.745,1,0,866.4 +M099d0,A/Chester/5355/2022,plate11-AAAAAACGCATGTAGA,0.001728,interpolated,0.001746,16.71,0.9199,0,578.8 +M099d0,A/Chester/5355/2022,plate11-CCTCAAAATAACAAGC,0.00176,interpolated,0.001779,20.74,0.8988,0,568.3 +M099d0,A/Chester/5355/2022,plate11-TCATATAAAGAAAAGG,0.001726,interpolated,0.001738,20.91,0.9337,0,579.5 +M099d0,A/Cote_DIvoire/1448/2021,plate11-GTCCGTTGATAAAGAG,0.001604,interpolated,0.001631,24.97,0.8257,0,623.6 +M099d0,A/Cote_DIvoire/1448/2021,plate11-GTTAAACGATCTATAG,0.001621,interpolated,0.001648,17.09,0.8753,0,617 +M099d0,A/Cote_DIvoire/1448/2021,plate11-TCGAGAACACCCATAA,0.0007473,interpolated,0.0008004,3.995,0.8801,0,1338 +M099d0,A/England/220200318/2022,plate11-CGTAATACATTTAAGA,0.0009549,interpolated,0.0009482,1.715,1.006,0,1047 +M099d0,A/England/220200318/2022,plate11-GACCAACTGTGGTACA,0.0005759,interpolated,0.0006202,2.643,0.9109,0,1737 +M099d0,A/England/220200318/2022,plate11-GCTGCGCCTAACATAA,0.001579,interpolated,0.001587,23.22,0.9449,0,633.2 +M099d0,A/Ghana/138/2020,plate11-CCAGTTCCCTTCGATG,0.001682,interpolated,0.001706,16.79,0.893,0,594.6 +M099d0,A/Ghana/138/2020,plate11-GACTATGGTCTAAAAA,0.0009391,interpolated,0.001048,4.822,0.7941,0,1065 +M099d0,A/Ghana/138/2020,plate11-TAAGCCATAAATCAAT,0.001027,interpolated,0.001123,3.442,0.8684,0,973.4 +M099d0,A/Ghana/2080/2020,plate11-CAGCAAAAGCATCACC,0.001668,interpolated,0.001685,18.55,0.9135,0,599.6 +M099d0,A/Ghana/2080/2020,plate11-GCAATCCCGCAATTTG,0.001404,interpolated,0.001404,3.93,1,0,712.3 +M099d0,A/Ghana/2080/2020,plate11-GTAGTGCATCATTGAT,0.001606,interpolated,0.001629,17.64,0.8889,0,622.7 +M099d0,A/Hawaii/70/2019,plate11-ACATGAATTCAGACGG,0.0008746,interpolated,0.0008718,2.613,1.004,0,1143 +M099d0,A/Hawaii/70/2019,plate11-AGTAAACATGCATTGG,0.00151,interpolated,0.001515,22.96,0.963,0,662.1 +M099d0,A/Hawaii/70/2019,plate11-ATAGAATCGCAAATTA,0.001637,interpolated,0.001644,21.96,0.954,0,610.9 +M099d0,A/Hawaii/70/2019,plate11-TGGAATCGTCACCGAT,0.000651,interpolated,0.0007103,3.498,0.8687,0,1536 +M099d0,A/India-PUN-NIV328484/2021,plate11-GATCTAATAATACGGC,0.001737,interpolated,0.001771,17.08,0.8614,0,575.6 +M099d0,A/India-PUN-NIV328484/2021,plate11-TCTGTTCCGGCCCGAA,0.001806,interpolated,0.001819,18.86,0.9357,0,553.8 +M099d0,A/India-PUN-NIV328484/2021,plate11-TTGTCCCGAGACAACA,0.002127,interpolated,0.002146,12.76,0.9463,0,470.1 +M099d0,A/India-Pune-Nivcov2221170/2022,plate11-AAATCTACCGCATTAT,0.004771,interpolated,0.004808,16.61,0.9403,0,209.6 +M099d0,A/India-Pune-Nivcov2221170/2022,plate11-CGTTTAAACAATGAAG,0.003635,interpolated,0.003745,3.013,0.9571,0,275.1 +M099d0,A/India/Pun-NIV312851/2021,plate11-ACAGCAAATACTCACA,0.002749,interpolated,0.002854,8.179,0.8683,0,363.8 +M099d0,A/India/Pun-NIV312851/2021,plate11-CAAGAACCCAAATATA,0.002309,interpolated,0.00241,3.339,0.9333,0,433.1 +M099d0,A/India/Pun-NIV312851/2021,plate11-GTAGCTATAACTAATA,0.001874,interpolated,0.001891,4.609,0.9791,0,533.6 +M099d0,A/Michigan/19/2021,plate11-AACGTTAACAAATGAA,0.001045,interpolated,0.001162,2.537,0.8822,0,956.9 +M099d0,A/Michigan/19/2021,plate11-AGAGAAAAAACAGTGA,0.001478,interpolated,0.001704,2.671,0.8421,0,676.4 +M099d0,A/Michigan/19/2021,plate11-TAATGAGCTTTATGGT,0.001792,interpolated,0.001801,15.38,0.9644,0,557.9 +M099d0,A/Michigan/45/2015,plate11-ACAAAGTCTCGAGAAG,0.0006212,interpolated,0.0006453,3.149,0.9435,0,1610 +M099d0,A/Michigan/45/2015,plate11-CACCTAGGATCGCACT,0.0008996,interpolated,0.0009483,4.403,0.8965,0,1112 +M099d0,A/Michigan/45/2015,plate11-TGAGGATAATCACAAG,0.001034,interpolated,0.0011,2.428,0.9308,0,967 +M099d0,A/Michigan/45/2015,plate11-TTGAAAAAATCATAAA,0.0006738,interpolated,0.0007125,3.664,0.9074,0,1484 +M099d0,A/Newcastle/2/2022,plate11-CAAATATATCTTCATG,0.002344,interpolated,0.002515,3.413,0.8931,0,426.7 +M099d0,A/Newcastle/2/2022,plate11-GCCCAAGTAGGTGCAA,0.002545,interpolated,0.002652,3.463,0.9334,0,392.9 +M099d0,A/Newcastle/2/2022,plate11-TTCACTAAGATTTCAT,0.001789,interpolated,0.001807,16.8,0.9234,0,559 +M099d0,A/Niger/10217/2021,plate11-AAATAAGTACGCAAAT,0.001029,interpolated,0.001041,5.597,0.969,0,972.1 +M099d0,A/Niger/10217/2021,plate11-CATCAACCGCCATTTC,0.001714,interpolated,0.001718,18.42,0.9789,0,583.4 +M099d0,A/Niger/10217/2021,plate11-GAACGATTGTAATTTT,0.001324,interpolated,0.001327,4.772,0.9933,0,755.4 +M099d0,A/Nimes/871/2021,plate11-ACCTTACTAAATCCTG,0.0005987,interpolated,0.000604,16.99,0.9302,0,1670 +M099d0,A/Nimes/871/2021,plate11-GTTCCTTTAAGCCAAA,0.0008267,interpolated,0.0009015,3.794,0.8599,0,1210 +M099d0,A/Nimes/871/2021,plate11-TAATTACATTGCGGTT,0.0005958,interpolated,0.000608,18.53,0.8427,0,1679 +M099d0,A/Norway/25089/2022,plate11-CGGATAAAAATGATAT,0.0008314,interpolated,0.0008314,5.001,1,0,1203 +M099d0,A/Norway/25089/2022,plate11-GACTCAATAATCACAC,0.003657,interpolated,0.004153,2.548,0.8617,0,273.4 +M099d0,A/Norway/25089/2022,plate11-TGGAAAAGATGTAATA,0.001788,interpolated,0.001795,16.64,0.9702,0,559.2 +M099d0,A/Paris/30353/2021,plate11-ACATAAGAACCCTATA,0.001716,interpolated,0.001726,16.65,0.9567,0,582.7 +M099d0,A/Paris/30353/2021,plate11-ACATTTCCCTCGATAT,0.001209,interpolated,0.001208,6.091,1.003,0,827.1 +M099d0,A/Paris/30353/2021,plate11-GTTTGACAATCACTAC,0.0008659,interpolated,0.000906,4.094,0.9154,0,1155 +M099d0,A/Paris/31196/2021,plate11-AAACTAAAAGCAAGGG,0.0009719,interpolated,0.001036,2.62,0.9231,0,1029 +M099d0,A/Paris/31196/2021,plate11-AATAAGTATACGGGAT,0.0008691,interpolated,0.000919,3.423,0.9131,0,1151 +M099d0,A/Paris/31196/2021,plate11-AGCAGCCTGAAAATAT,0.0005939,interpolated,0.0005935,4.693,1.001,0,1684 +M099d0,A/Perth/1/2022,plate11-AGCCCCGTGAGAAGCA,0.001802,interpolated,0.001821,20.18,0.9013,0,555 +M099d0,A/Perth/1/2022,plate11-CTGCACGAGAGACTTC,0.001956,interpolated,0.001972,14.03,0.9477,0,511.1 +M099d0,A/Perth/1/2022,plate11-TTGGGGAAATATATAA,0.001835,interpolated,0.001887,2.601,0.9651,0,544.9 +M099d0,A/SouthAfrica/R14850/2021,plate11-AACTCCGCAGACACTG,0.001722,interpolated,0.001736,15.91,0.9394,0,580.6 +M099d0,A/SouthAfrica/R14850/2021,plate11-GAGACGTACGAAATTA,0.001813,interpolated,0.00183,18.35,0.9178,0,551.7 +M099d0,A/SouthAfrica/R14850/2021,plate11-TACTCAACAAGATAAA,0.00177,interpolated,0.001775,16.27,0.9781,0,565 +M099d0,A/SouthAfrica/R16462/2021,plate11-CACCATTAAAGAGGTA,0.00152,interpolated,0.00152,11.5,1,0,658 +M099d0,A/SouthAfrica/R16462/2021,plate11-CGGCGTATCGTTCACA,0.00154,interpolated,0.001551,26.23,0.9087,0,649.5 +M099d0,A/SouthAfrica/R16462/2021,plate11-CTAGCAGATTGTATAA,0.000824,interpolated,0.0008255,3.401,0.9969,0,1214 +M099d0,A/Sydney/43/2022,plate11-CTATTAATCATGCAAA,0.002259,interpolated,0.00246,5.518,0.8126,0,442.7 +M099d0,A/Sydney/43/2022,plate11-TACGGACATTCTTAAC,0.003375,interpolated,0.003448,4.837,0.951,0,296.3 +M099d0,A/Sydney/43/2022,plate11-TAGTATAATAGAGCAG,0.004849,interpolated,0.004871,22.71,0.9495,0,206.2 +M099d0,A/Togo/0274/2021,plate11-AACGAATGAATTTCTT,0.001043,interpolated,0.001153,3.61,0.8479,0,959 +M099d0,A/Togo/0274/2021,plate11-GTAACATTATACGATT,0.001011,interpolated,0.00101,3.268,1.001,0,989.5 +M099d0,A/Togo/0274/2021,plate11-TAGCAGATGTATCAAT,0.0008495,interpolated,0.0009267,2.682,0.896,0,1177 +M099d0,A/Togo/0304/2021,plate11-AACTCTAAAGATATAA,0.001628,interpolated,0.001631,19.15,0.984,0,614.2 +M099d0,A/Togo/0304/2021,plate11-AGAGATAATAACAAAA,0.00157,interpolated,0.001585,19.32,0.9148,0,637 +M099d0,A/Togo/0304/2021,plate11-GAAGAATGGTTTTCTG,0.0007614,interpolated,0.0007598,3.113,1.003,0,1313 +M099d0,A/Togo/845/2020,plate11-AGGTCAAGACCACAGG,0.001196,interpolated,0.001326,3.08,0.864,0,836 +M099d0,A/Togo/845/2020,plate11-GCATGGATCCTTTACT,0.0006089,interpolated,0.0006157,14.93,0.9241,0,1642 +M099d0,A/Togo/845/2020,plate11-TTACCGTCTACGCATA,0.0007218,interpolated,0.0007523,3.46,0.9333,0,1385 +M099d0,A/Utah/27/2022,plate11-ACAATGTGACTCACCC,0.002152,interpolated,0.002174,4.635,0.9767,0,464.7 +M099d0,A/Utah/27/2022,plate11-TAAATAACTCGTATTT,0.004301,interpolated,0.00463,1.195,0.9578,0,232.5 +M099d0,A/Utah/27/2022,plate11-TCCTTGTAATTCAACT,0.003346,interpolated,0.003321,1.741,1.007,0,298.9 +M099d0,A/Washington/23/2020,plate11-ACGGAATCCCCTGAGA,0.001956,interpolated,0.001964,16.18,0.9684,0,511.3 +M099d0,A/Washington/23/2020,plate11-GAACTGGCGTCAATCA,0.001561,interpolated,0.001667,13.78,0.7015,0,640.7 +M099d0,A/Washington/23/2020,plate11-GGATAAGAAAACTACT,0.00184,interpolated,0.001862,18.96,0.8976,0,543.6 +M099d0,A/Wisconsin/588/2019,plate11-AGTCCTATCCTCAAAT,0.0006832,interpolated,0.0007434,1.707,0.9329,0,1464 +M099d0,A/Wisconsin/588/2019,plate11-GAAGAAACTATAACCA,0.002637,interpolated,0.002673,3.913,0.9742,0,379.3 +M099d0,A/Wisconsin/588/2019,plate11-TATATTAGTAACATAA,0.001759,interpolated,0.00177,20.26,0.9387,0,568.5 +M099d30,A/Bangladesh/2221/2021,plate11-AAGAGAAATATTCGCT,0.001545,interpolated,0.001571,18.99,0.8633,0,647.2 +M099d30,A/Bangladesh/2221/2021,plate11-GACAGCAATGCATACA,0.0005474,interpolated,0.0005607,17.32,0.8293,0,1827 +M099d30,A/Bangladesh/2221/2021,plate11-GATAGAAATACCAGGA,0.0005683,interpolated,0.0005712,21.26,0.9479,0,1760 +M099d30,A/Bangladesh/3210810034/2021,plate11-AACTATAGATCTAGAA,0.0009288,interpolated,0.0009284,3.594,1.001,0,1077 +M099d30,A/Bangladesh/3210810034/2021,plate11-ACAAAAGTACCTCTAC,0.0006498,interpolated,0.0006754,2.149,0.9602,0,1539 +M099d30,A/Bangladesh/8002/2021,plate11-AGTGTCCCTAAGAGGC,0.0006305,interpolated,0.0006333,16.55,0.9649,0,1586 +M099d30,A/Bangladesh/8002/2021,plate11-GCAACGCCAAATAATT,0.001543,interpolated,0.001563,22.73,0.871,0,648.2 +M099d30,A/Bangladesh/8002/2021,plate11-TCTGCTAAACTAAGTA,0.0005829,interpolated,0.0006193,20.13,0.6476,0,1716 +M099d30,A/Bangladesh/8036/2021,plate11-ACGGGGCCCAGGTAAT,0.0005946,interpolated,0.000595,16.82,0.9946,0,1682 +M099d30,A/Bangladesh/8036/2021,plate11-ATACCTCAACCTTGAA,0.000704,interpolated,0.0007206,2.396,0.9728,0,1420 +M099d30,A/Bangladesh/8036/2021,plate11-CAGTTCTGCGACCAGC,0.0005947,interpolated,0.0006119,19.31,0.7884,0,1681 +M099d30,A/Belgium/H0017/2022,plate11-AATGAAAGTTAGCATT,0.000553,interpolated,0.000559,17.12,0.9153,0,1808 +M099d30,A/Belgium/H0017/2022,plate11-ATGTCCATAAAAAATA,0.0006154,interpolated,0.0006165,20.06,0.983,0,1625 +M099d30,A/Belgium/H0017/2022,plate11-GTAAAGCAAATCCATT,0.0005325,interpolated,0.0005438,18.84,0.8371,0,1878 +M099d30,A/Belgium/H0038/2022,plate11-GATCCGTACTTTGATT,0.0006796,interpolated,0.0006942,13.95,0.872,0,1471 +M099d30,A/Belgium/H0038/2022,plate11-GCCGGAGGGCATTTTC,0.0005912,interpolated,0.0006008,20.52,0.859,0,1692 +M099d30,A/Belgium/H0038/2022,plate11-TACCGTATAATTAAAA,0.0005335,interpolated,0.0005818,21.25,0.5793,0,1874 +M099d30,A/Brisbane/02/2018,plate11-ACGACATGATCAAACG,0.0001906,interpolated,0.0002394,2.371,0.791,0,5248 +M099d30,A/Brisbane/02/2018,plate11-ATCCGATTTAAAGGCA,0.0005508,interpolated,0.0005667,25.77,0.7398,0,1816 +M099d30,A/Brisbane/02/2018,plate11-TAATAAGCCAGCAAGA,0.0001579,interpolated,0.0001547,1.193,1.012,0,6334 +M099d30,A/Brisbane/02/2018,plate11-TTGGGCACTAAATTAA,0.000277,interpolated,0.0003768,2.246,0.7505,0,3611 +M099d30,A/Brisbane/48/2022,plate11-CCCTATGCTGCGTATT,0.0006428,interpolated,0.0006674,14.77,0.787,0,1556 +M099d30,A/Brisbane/48/2022,plate11-GAGCTCTAAAGCAACA,0.0007285,interpolated,0.0008109,2.748,0.8725,0,1373 +M099d30,A/Brisbane/48/2022,plate11-TTATGATCTAAACAGA,0.000705,interpolated,0.0008648,2.222,0.8176,0,1418 +M099d30,A/California/07/2009,plate11-CATGTGAATTCGCCCA,0.0001335,interpolated,0.0001628,1.26,0.8896,0,7489 +M099d30,A/California/07/2009,plate11-CCTTTCTCAAAACATA,0.0003109,interpolated,0.0003625,3.298,0.8013,0,3216 +M099d30,A/California/07/2009,plate11-CGCCTAATGTTAATAA,0.000548,interpolated,0.0005563,20.08,0.8705,0,1825 +M099d30,A/California/07/2009,plate11-GACACAGAACCCATGC,0.0002822,interpolated,0.0002994,2.659,0.9271,0,3543 +M099d30,A/Chester/5355/2022,plate11-AAAAAACGCATGTAGA,0.0009585,interpolated,0.001145,1.874,0.8584,0,1043 +M099d30,A/Chester/5355/2022,plate11-CCTCAAAATAACAAGC,0.0001835,interpolated,0.0002277,0.8833,0.9132,0,5450 +M099d30,A/Chester/5355/2022,plate11-TCATATAAAGAAAAGG,0.0005978,interpolated,0.0006277,16.79,0.7206,0,1673 +M099d30,A/Cote_DIvoire/1448/2021,plate11-GTCCGTTGATAAAGAG,0.0003411,interpolated,0.0004246,2.341,0.7995,0,2931 +M099d30,A/Cote_DIvoire/1448/2021,plate11-GTTAAACGATCTATAG,0.0005078,interpolated,0.0005078,10.54,1,0,1969 +M099d30,A/Cote_DIvoire/1448/2021,plate11-TCGAGAACACCCATAA,0.0005347,interpolated,0.0005962,20.34,0.5546,0,1870 +M099d30,A/England/220200318/2022,plate11-CGTAATACATTTAAGA,0.000508,interpolated,0.000508,15.19,1,0,1969 +M099d30,A/England/220200318/2022,plate11-GACCAACTGTGGTACA,0.0005249,interpolated,0.0005304,22.18,0.8961,0,1905 +M099d30,A/England/220200318/2022,plate11-GCTGCGCCTAACATAA,0.0006058,interpolated,0.0006173,22.18,0.8301,0,1651 +M099d30,A/Ghana/138/2020,plate11-CCAGTTCCCTTCGATG,0.0005838,interpolated,0.000591,23.29,0.8761,0,1713 +M099d30,A/Ghana/138/2020,plate11-GACTATGGTCTAAAAA,0.0005841,interpolated,0.0005933,21.13,0.8585,0,1712 +M099d30,A/Ghana/138/2020,plate11-TAAGCCATAAATCAAT,0.0005764,interpolated,0.0005788,17.66,0.9641,0,1735 +M099d30,A/Ghana/2080/2020,plate11-CAGCAAAAGCATCACC,0.0003454,interpolated,0.000377,1.848,0.9254,0,2895 +M099d30,A/Ghana/2080/2020,plate11-GCAATCCCGCAATTTG,0.0003528,interpolated,0.0003571,7.882,0.9539,0,2835 +M099d30,A/Ghana/2080/2020,plate11-GTAGTGCATCATTGAT,0.0003275,interpolated,0.0003555,5.621,0.8153,0,3053 +M099d30,A/Hawaii/70/2019,plate11-ACATGAATTCAGACGG,0.0005528,interpolated,0.0005553,19.69,0.9565,0,1809 +M099d30,A/Hawaii/70/2019,plate11-AGTAAACATGCATTGG,0.0004447,interpolated,0.0004715,4.373,0.8872,0,2249 +M099d30,A/Hawaii/70/2019,plate11-ATAGAATCGCAAATTA,0.0003734,interpolated,0.0004301,3.033,0.8255,0,2678 +M099d30,A/Hawaii/70/2019,plate11-TGGAATCGTCACCGAT,0.0002158,interpolated,0.0002121,2.125,1.019,0,4635 +M099d30,A/India-PUN-NIV328484/2021,plate11-GATCTAATAATACGGC,0.000186,interpolated,0.0002322,1.005,0.9001,0,5376 +M099d30,A/India-PUN-NIV328484/2021,plate11-TCTGTTCCGGCCCGAA,0.0006103,interpolated,0.0006189,20.37,0.8751,0,1639 +M099d30,A/India-PUN-NIV328484/2021,plate11-TTGTCCCGAGACAACA,0.0005508,interpolated,0.0005529,18.33,0.9659,0,1816 +M099d30,A/India-Pune-Nivcov2221170/2022,plate11-AAATCTACCGCATTAT,0.000945,interpolated,0.0009789,4.183,0.9314,0,1058 +M099d30,A/India-Pune-Nivcov2221170/2022,plate11-CGTTTAAACAATGAAG,0.001045,interpolated,0.001119,4.497,0.8682,0,956.9 +M099d30,A/India/Pun-NIV312851/2021,plate11-ACAGCAAATACTCACA,0.0002109,interpolated,0.0002502,3.096,0.7946,0,4743 +M099d30,A/India/Pun-NIV312851/2021,plate11-CAAGAACCCAAATATA,0.0006684,interpolated,0.000703,13.58,0.7519,0,1496 +M099d30,A/India/Pun-NIV312851/2021,plate11-GTAGCTATAACTAATA,0.0007989,interpolated,0.000819,3.695,0.9559,0,1252 +M099d30,A/Michigan/19/2021,plate11-AACGTTAACAAATGAA,0.0005813,interpolated,0.0005947,19.83,0.8178,0,1720 +M099d30,A/Michigan/19/2021,plate11-AGAGAAAAAACAGTGA,0.0005911,interpolated,0.000604,19.94,0.8249,0,1692 +M099d30,A/Michigan/19/2021,plate11-TAATGAGCTTTATGGT,0.0005334,interpolated,0.0005346,2.923,0.9968,0,1875 +M099d30,A/Michigan/45/2015,plate11-ACAAAGTCTCGAGAAG,0.0002053,interpolated,0.0002311,1.393,0.9239,0,4872 +M099d30,A/Michigan/45/2015,plate11-CACCTAGGATCGCACT,0.000181,interpolated,0.000192,2.06,0.9427,0,5526 +M099d30,A/Michigan/45/2015,plate11-TGAGGATAATCACAAG,0.0001948,interpolated,0.0002034,3.932,0.9218,0,5134 +M099d30,A/Michigan/45/2015,plate11-TTGAAAAAATCATAAA,6.159e-05,interpolated,9.749e-05,1.036,0.8106,0,1.624e+04 +M099d30,A/Newcastle/2/2022,plate11-CAAATATATCTTCATG,0.0003577,interpolated,0.0003527,1.174,1.008,0,2796 +M099d30,A/Newcastle/2/2022,plate11-GCCCAAGTAGGTGCAA,0.0007586,interpolated,0.0007863,7.082,0.8876,0,1318 +M099d30,A/Newcastle/2/2022,plate11-TTCACTAAGATTTCAT,0.001483,interpolated,0.001494,31.29,0.9025,0,674.1 +M099d30,A/Niger/10217/2021,plate11-AAATAAGTACGCAAAT,0.0005801,interpolated,0.0005872,19.98,0.8917,0,1724 +M099d30,A/Niger/10217/2021,plate11-CATCAACCGCCATTTC,0.0006661,interpolated,0.0006749,2.765,0.9822,0,1501 +M099d30,A/Niger/10217/2021,plate11-GAACGATTGTAATTTT,0.000595,interpolated,0.0006,17.78,0.9306,0,1681 +M099d30,A/Nimes/871/2021,plate11-ACCTTACTAAATCCTG,0.0003188,interpolated,0.0003376,3.328,0.9131,0,3137 +M099d30,A/Nimes/871/2021,plate11-GTTCCTTTAAGCCAAA,0.0003769,interpolated,0.0003989,3.019,0.9213,0,2653 +M099d30,A/Nimes/871/2021,plate11-TAATTACATTGCGGTT,0.0002387,interpolated,0.0003045,4.034,0.6872,0,4189 +M099d30,A/Norway/25089/2022,plate11-CGGATAAAAATGATAT,0.003885,interpolated,0.00395,29.03,0.8087,0,257.4 +M099d30,A/Norway/25089/2022,plate11-GACTCAATAATCACAC,0.001394,interpolated,0.002091,2.847,0.6577,0,717.1 +M099d30,A/Norway/25089/2022,plate11-TGGAAAAGATGTAATA,0.003951,interpolated,0.003951,19.52,1,0,253.1 +M099d30,A/Paris/30353/2021,plate11-ACATAAGAACCCTATA,0.0005933,interpolated,0.0005952,16.04,0.9755,0,1685 +M099d30,A/Paris/30353/2021,plate11-ACATTTCCCTCGATAT,0.0007984,interpolated,0.0008234,7.385,0.898,0,1253 +M099d30,A/Paris/30353/2021,plate11-GTTTGACAATCACTAC,0.0005857,interpolated,0.000591,16.69,0.9299,0,1707 +M099d30,A/Paris/31196/2021,plate11-AAACTAAAAGCAAGGG,0.0006933,interpolated,0.0007629,6.413,0.7708,0,1442 +M099d30,A/Paris/31196/2021,plate11-AATAAGTATACGGGAT,9.664e-05,interpolated,0.0001494,1.083,0.8119,0,1.035e+04 +M099d30,A/Paris/31196/2021,plate11-AGCAGCCTGAAAATAT,0.0005637,interpolated,0.0005776,21.24,0.7982,0,1774 +M099d30,A/Perth/1/2022,plate11-AGCCCCGTGAGAAGCA,0.0005847,interpolated,0.0006025,16.46,0.8055,0,1710 +M099d30,A/Perth/1/2022,plate11-CTGCACGAGAGACTTC,0.0005929,interpolated,0.0005939,18.8,0.9854,0,1686 +M099d30,A/Perth/1/2022,plate11-TTGGGGAAATATATAA,0.0006368,interpolated,0.0006484,15.69,0.877,0,1570 +M099d30,A/SouthAfrica/R14850/2021,plate11-AACTCCGCAGACACTG,0.001005,interpolated,0.001036,2.763,0.9603,0,994.9 +M099d30,A/SouthAfrica/R14850/2021,plate11-GAGACGTACGAAATTA,0.001597,interpolated,0.001631,20.96,0.8239,0,626.1 +M099d30,A/SouthAfrica/R14850/2021,plate11-TACTCAACAAGATAAA,0.001632,interpolated,0.001632,10.26,1,0,612.9 +M099d30,A/SouthAfrica/R16462/2021,plate11-CACCATTAAAGAGGTA,0.0005869,interpolated,0.0006267,2.771,0.9169,0,1704 +M099d30,A/SouthAfrica/R16462/2021,plate11-CGGCGTATCGTTCACA,0.0005728,interpolated,0.0005946,19.74,0.739,0,1746 +M099d30,A/SouthAfrica/R16462/2021,plate11-CTAGCAGATTGTATAA,0.0005442,interpolated,0.0005462,19.62,0.9664,0,1837 +M099d30,A/Sydney/43/2022,plate11-CTATTAATCATGCAAA,0.00155,interpolated,0.00157,21.49,0.8808,0,645.1 +M099d30,A/Sydney/43/2022,plate11-TACGGACATTCTTAAC,0.0008352,interpolated,0.000887,3.015,0.9171,0,1197 +M099d30,A/Sydney/43/2022,plate11-TAGTATAATAGAGCAG,0.0008496,interpolated,0.0008684,7.355,0.9259,0,1177 +M099d30,A/Togo/0274/2021,plate11-AACGAATGAATTTCTT,0.0005516,interpolated,0.0005706,18.35,0.7692,0,1813 +M099d30,A/Togo/0274/2021,plate11-GTAACATTATACGATT,0.0005406,interpolated,0.0005513,21.88,0.8248,0,1850 +M099d30,A/Togo/0274/2021,plate11-TAGCAGATGTATCAAT,0.0003746,interpolated,0.0004142,1.773,0.9185,0,2669 +M099d30,A/Togo/0304/2021,plate11-AACTCTAAAGATATAA,0.0005406,interpolated,0.000634,2.454,0.8381,0,1850 +M099d30,A/Togo/0304/2021,plate11-AGAGATAATAACAAAA,0.0005774,interpolated,0.0005767,4.172,1.003,0,1732 +M099d30,A/Togo/0304/2021,plate11-GAAGAATGGTTTTCTG,0.000554,interpolated,0.0005557,17.21,0.974,0,1805 +M099d30,A/Togo/845/2020,plate11-AGGTCAAGACCACAGG,0.000585,interpolated,0.000585,7.888,1,0,1709 +M099d30,A/Togo/845/2020,plate11-GCATGGATCCTTTACT,0.0006018,interpolated,0.0006059,18.52,0.9414,0,1662 +M099d30,A/Togo/845/2020,plate11-TTACCGTCTACGCATA,0.0005746,interpolated,0.0005835,19.5,0.8705,0,1740 +M099d30,A/Utah/27/2022,plate11-ACAATGTGACTCACCC,0.0007682,interpolated,0.0007682,5.132,1,0,1302 +M099d30,A/Utah/27/2022,plate11-TAAATAACTCGTATTT,0.0008124,interpolated,0.0008276,3.273,0.9705,0,1231 +M099d30,A/Utah/27/2022,plate11-TCCTTGTAATTCAACT,0.0007829,interpolated,0.0007877,5.961,0.9819,0,1277 +M099d30,A/Washington/23/2020,plate11-ACGGAATCCCCTGAGA,0.001069,interpolated,0.001069,30.9,1,0,935.6 +M099d30,A/Washington/23/2020,plate11-GAACTGGCGTCAATCA,0.0004936,interpolated,0.0005492,22.1,0.5471,0,2026 +M099d30,A/Washington/23/2020,plate11-GGATAAGAAAACTACT,0.0005574,interpolated,0.0005719,20.62,0.795,0,1794 +M099d30,A/Wisconsin/588/2019,plate11-AGTCCTATCCTCAAAT,0.0003529,interpolated,0.0004355,1.628,0.855,0,2834 +M099d30,A/Wisconsin/588/2019,plate11-GAAGAAACTATAACCA,0.0006004,interpolated,0.0006013,21.75,0.9842,0,1666 +M099d30,A/Wisconsin/588/2019,plate11-TATATTAGTAACATAA,0.0005371,interpolated,0.0005666,17.76,0.6936,0,1862 +Y044d30,A/Bangladesh/2221/2021,plate11-AAGAGAAATATTCGCT,0.0002399,interpolated,0.0002378,1.477,1.007,0,4168 +Y044d30,A/Bangladesh/2221/2021,plate11-GACAGCAATGCATACA,0.0004705,interpolated,0.0004702,2.877,1.001,0,2125 +Y044d30,A/Bangladesh/2221/2021,plate11-GATAGAAATACCAGGA,0.0008471,interpolated,0.0008471,9.086,1,0,1180 +Y044d30,A/Bangladesh/3210810034/2021,plate11-AACTATAGATCTAGAA,0.001659,interpolated,0.001659,4.99,1,0,602.7 +Y044d30,A/Bangladesh/3210810034/2021,plate11-ACAAAAGTACCTCTAC,0.002138,interpolated,0.002138,2.69,1,0,467.6 +Y044d30,A/Bangladesh/8002/2021,plate11-AGTGTCCCTAAGAGGC,0.001104,interpolated,0.001106,13.42,0.9882,0,905.5 +Y044d30,A/Bangladesh/8002/2021,plate11-GCAACGCCAAATAATT,0.0008309,interpolated,0.0008309,9.171,1,0,1204 +Y044d30,A/Bangladesh/8002/2021,plate11-TCTGCTAAACTAAGTA,0.0007821,interpolated,0.0007821,9.569,1,0,1279 +Y044d30,A/Bangladesh/8036/2021,plate11-ACGGGGCCCAGGTAAT,0.0006094,interpolated,0.0006094,16,1,0,1641 +Y044d30,A/Bangladesh/8036/2021,plate11-ATACCTCAACCTTGAA,0.0008283,interpolated,0.0008283,8.014,1,0,1207 +Y044d30,A/Bangladesh/8036/2021,plate11-CAGTTCTGCGACCAGC,0.0001966,interpolated,0.0001974,18.04,0.9677,0,5086 +Y044d30,A/Belgium/H0017/2022,plate11-AATGAAAGTTAGCATT,7.985e-05,interpolated,8.018e-05,5.855,0.9878,0,1.252e+04 +Y044d30,A/Belgium/H0017/2022,plate11-ATGTCCATAAAAAATA,6.046e-05,interpolated,6.042e-05,5.476,1.002,0,1.654e+04 +Y044d30,A/Belgium/H0017/2022,plate11-GTAAAGCAAATCCATT,6.929e-05,interpolated,6.923e-05,4.61,1.002,0,1.443e+04 +Y044d30,A/Belgium/H0038/2022,plate11-GATCCGTACTTTGATT,6.936e-05,interpolated,6.981e-05,15.9,0.951,0,1.442e+04 +Y044d30,A/Belgium/H0038/2022,plate11-GCCGGAGGGCATTTTC,7.477e-05,interpolated,7.575e-05,3.956,0.975,0,1.337e+04 +Y044d30,A/Belgium/H0038/2022,plate11-TACCGTATAATTAAAA,6.633e-05,interpolated,6.763e-05,19.28,0.8442,0,1.508e+04 +Y044d30,A/Brisbane/02/2018,plate11-ACGACATGATCAAACG,9.756e-05,interpolated,0.0001028,2.157,0.947,0,1.025e+04 +Y044d30,A/Brisbane/02/2018,plate11-ATCCGATTTAAAGGCA,6.424e-05,interpolated,6.225e-05,2.014,1.033,0,1.557e+04 +Y044d30,A/Brisbane/02/2018,plate11-TAATAAGCCAGCAAGA,0.0001361,interpolated,0.0001361,3.598,1.001,0,7348 +Y044d30,A/Brisbane/02/2018,plate11-TTGGGCACTAAATTAA,5.457e-05,interpolated,5.439e-05,4.346,1.007,0,1.832e+04 +Y044d30,A/Brisbane/48/2022,plate11-CCCTATGCTGCGTATT,0.001013,interpolated,0.001013,5.499,1,0,986.9 +Y044d30,A/Brisbane/48/2022,plate11-GAGCTCTAAAGCAACA,0.001242,interpolated,0.001261,10.52,0.9292,0,804.9 +Y044d30,A/Brisbane/48/2022,plate11-TTATGATCTAAACAGA,0.0002522,interpolated,0.0002524,14.37,0.9931,0,3965 +Y044d30,A/California/07/2009,plate11-CATGTGAATTCGCCCA,0.0001336,interpolated,0.0001331,2.392,1.005,0,7484 +Y044d30,A/California/07/2009,plate11-CCTTTCTCAAAACATA,6.417e-05,interpolated,6.306e-05,2.51,1.022,0,1.558e+04 +Y044d30,A/California/07/2009,plate11-CGCCTAATGTTAATAA,0.0001411,interpolated,0.0001384,1.628,1.016,0,7087 +Y044d30,A/California/07/2009,plate11-GACACAGAACCCATGC,9.119e-05,interpolated,8.857e-05,1.77,1.026,0,1.097e+04 +Y044d30,A/Chester/5355/2022,plate11-AAAAAACGCATGTAGA,0.0004981,interpolated,0.0005175,3.823,0.932,0,2008 +Y044d30,A/Chester/5355/2022,plate11-CCTCAAAATAACAAGC,0.001262,interpolated,0.00128,12.91,0.918,0,792.3 +Y044d30,A/Chester/5355/2022,plate11-TCATATAAAGAAAAGG,0.0002229,interpolated,0.0002246,15.86,0.9418,0,4487 +Y044d30,A/Cote_DIvoire/1448/2021,plate11-GTCCGTTGATAAAGAG,6.281e-05,interpolated,6.361e-05,17.49,0.901,0,1.592e+04 +Y044d30,A/Cote_DIvoire/1448/2021,plate11-GTTAAACGATCTATAG,8.656e-05,interpolated,8.652e-05,4.307,1.001,0,1.155e+04 +Y044d30,A/Cote_DIvoire/1448/2021,plate11-TCGAGAACACCCATAA,6.427e-05,interpolated,6.578e-05,17.27,0.8343,0,1.556e+04 +Y044d30,A/England/220200318/2022,plate11-CGTAATACATTTAAGA,6.733e-05,interpolated,6.733e-05,14.93,1,0,1.485e+04 +Y044d30,A/England/220200318/2022,plate11-GACCAACTGTGGTACA,6.403e-05,interpolated,6.433e-05,18.44,0.9581,0,1.562e+04 +Y044d30,A/England/220200318/2022,plate11-GCTGCGCCTAACATAA,5.883e-05,interpolated,5.877e-05,5.077,1.003,0,1.7e+04 +Y044d30,A/Ghana/138/2020,plate11-CCAGTTCCCTTCGATG,5.851e-05,interpolated,5.849e-05,6.519,1.001,0,1.709e+04 +Y044d30,A/Ghana/138/2020,plate11-GACTATGGTCTAAAAA,4.523e-05,interpolated,4.765e-05,3.397,0.9191,0,2.211e+04 +Y044d30,A/Ghana/138/2020,plate11-TAAGCCATAAATCAAT,6.69e-05,interpolated,6.708e-05,18.71,0.976,0,1.495e+04 +Y044d30,A/Ghana/2080/2020,plate11-CAGCAAAAGCATCACC,6.216e-05,interpolated,6.215e-05,6.481,1.001,0,1.609e+04 +Y044d30,A/Ghana/2080/2020,plate11-GCAATCCCGCAATTTG,6.414e-05,interpolated,6.443e-05,17.42,0.9618,0,1.559e+04 +Y044d30,A/Ghana/2080/2020,plate11-GTAGTGCATCATTGAT,6.299e-05,interpolated,6.299e-05,20.09,0.9992,0,1.588e+04 +Y044d30,A/Hawaii/70/2019,plate11-ACATGAATTCAGACGG,5.794e-05,interpolated,5.791e-05,5.722,1.002,0,1.726e+04 +Y044d30,A/Hawaii/70/2019,plate11-AGTAAACATGCATTGG,0.0001991,interpolated,0.0002012,14.32,0.9301,0,5022 +Y044d30,A/Hawaii/70/2019,plate11-ATAGAATCGCAAATTA,8.047e-05,interpolated,8.536e-05,3.364,0.91,0,1.243e+04 +Y044d30,A/Hawaii/70/2019,plate11-TGGAATCGTCACCGAT,6.602e-05,interpolated,6.725e-05,18.59,0.855,0,1.515e+04 +Y044d30,A/India-PUN-NIV328484/2021,plate11-GATCTAATAATACGGC,0.0001985,interpolated,0.0001994,18.26,0.9591,0,5037 +Y044d30,A/India-PUN-NIV328484/2021,plate11-TCTGTTCCGGCCCGAA,0.0008332,interpolated,0.0008332,8.307,1,0,1200 +Y044d30,A/India-PUN-NIV328484/2021,plate11-TTGTCCCGAGACAACA,0.001004,interpolated,0.001011,18.87,0.9448,0,995.6 +Y044d30,A/India-Pune-Nivcov2221170/2022,plate11-AAATCTACCGCATTAT,0.0006088,interpolated,0.0006088,21.48,1,0,1643 +Y044d30,A/India-Pune-Nivcov2221170/2022,plate11-CGTTTAAACAATGAAG,0.0008414,interpolated,0.0008414,10.51,1,0,1188 +Y044d30,A/India/Pun-NIV312851/2021,plate11-ACAGCAAATACTCACA,0.00111,interpolated,0.001128,13.04,0.9069,0,900.8 +Y044d30,A/India/Pun-NIV312851/2021,plate11-CAAGAACCCAAATATA,0.001121,interpolated,0.001139,12.86,0.9078,0,891.8 +Y044d30,A/India/Pun-NIV312851/2021,plate11-GTAGCTATAACTAATA,0.0007758,interpolated,0.0007758,8.016,1,0,1289 +Y044d30,A/Michigan/19/2021,plate11-AACGTTAACAAATGAA,0.001252,interpolated,0.001258,10.15,0.9771,0,798.8 +Y044d30,A/Michigan/19/2021,plate11-AGAGAAAAAACAGTGA,0.001079,interpolated,0.001089,12.6,0.9466,0,926.6 +Y044d30,A/Michigan/19/2021,plate11-TAATGAGCTTTATGGT,0.0007932,interpolated,0.0007932,8.468,1,0,1261 +Y044d30,A/Michigan/45/2015,plate11-ACAAAGTCTCGAGAAG,7.119e-05,interpolated,7.079e-05,3.155,1.009,0,1.405e+04 +Y044d30,A/Michigan/45/2015,plate11-CACCTAGGATCGCACT,7.485e-05,interpolated,7.337e-05,2.191,1.022,0,1.336e+04 +Y044d30,A/Michigan/45/2015,plate11-TGAGGATAATCACAAG,6.165e-05,interpolated,6.157e-05,4.702,1.003,0,1.622e+04 +Y044d30,A/Michigan/45/2015,plate11-TTGAAAAAATCATAAA,0.0001044,interpolated,0.0001145,1.986,0.9166,0,9578 +Y044d30,A/Newcastle/2/2022,plate11-CAAATATATCTTCATG,0.001164,interpolated,0.001168,13.25,0.9763,0,859 +Y044d30,A/Newcastle/2/2022,plate11-GCCCAAGTAGGTGCAA,0.001334,interpolated,0.001343,7.91,0.9746,0,749.6 +Y044d30,A/Newcastle/2/2022,plate11-TTCACTAAGATTTCAT,0.0008486,interpolated,0.0008486,7.712,1,0,1178 +Y044d30,A/Niger/10217/2021,plate11-AAATAAGTACGCAAAT,8.475e-05,interpolated,8.459e-05,3.476,1.003,0,1.18e+04 +Y044d30,A/Niger/10217/2021,plate11-CATCAACCGCCATTTC,7.216e-05,interpolated,7.205e-05,4.058,1.003,0,1.386e+04 +Y044d30,A/Niger/10217/2021,plate11-GAACGATTGTAATTTT,9.047e-05,interpolated,9.041e-05,4.06,1.001,0,1.105e+04 +Y044d30,A/Nimes/871/2021,plate11-ACCTTACTAAATCCTG,6.495e-05,interpolated,6.259e-05,1.946,1.037,0,1.54e+04 +Y044d30,A/Nimes/871/2021,plate11-GTTCCTTTAAGCCAAA,6.642e-05,interpolated,6.68e-05,5.083,0.9856,0,1.506e+04 +Y044d30,A/Nimes/871/2021,plate11-TAATTACATTGCGGTT,6.526e-05,interpolated,6.542e-05,18.87,0.9773,0,1.532e+04 +Y044d30,A/Norway/25089/2022,plate11-CGGATAAAAATGATAT,0.0009003,interpolated,0.0009002,6.045,1,0,1111 +Y044d30,A/Norway/25089/2022,plate11-GACTCAATAATCACAC,0.001687,interpolated,0.001698,6.079,0.981,0,592.6 +Y044d30,A/Norway/25089/2022,plate11-TGGAAAAGATGTAATA,0.001072,interpolated,0.001072,3.634,1.001,0,932.6 +Y044d30,A/Paris/30353/2021,plate11-ACATAAGAACCCTATA,0.0001741,interpolated,0.0001741,15.98,1,0,5745 +Y044d30,A/Paris/30353/2021,plate11-ACATTTCCCTCGATAT,0.0001209,interpolated,0.0001205,2.586,1.004,0,8269 +Y044d30,A/Paris/30353/2021,plate11-GTTTGACAATCACTAC,5.85e-05,interpolated,5.849e-05,7.068,1,0,1.709e+04 +Y044d30,A/Paris/31196/2021,plate11-AAACTAAAAGCAAGGG,7.026e-05,interpolated,7.069e-05,17.37,0.949,0,1.423e+04 +Y044d30,A/Paris/31196/2021,plate11-AATAAGTATACGGGAT,7.751e-05,interpolated,7.74e-05,3.874,1.003,0,1.29e+04 +Y044d30,A/Paris/31196/2021,plate11-AGCAGCCTGAAAATAT,5.318e-05,interpolated,5.32e-05,8.04,0.9985,0,1.881e+04 +Y044d30,A/Perth/1/2022,plate11-AGCCCCGTGAGAAGCA,0.0003054,interpolated,0.0003058,2.722,0.9985,0,3274 +Y044d30,A/Perth/1/2022,plate11-CTGCACGAGAGACTTC,0.001,interpolated,0.001005,13.91,0.9651,0,999.8 +Y044d30,A/Perth/1/2022,plate11-TTGGGGAAATATATAA,0.001177,interpolated,0.00118,11.47,0.9862,0,849.3 +Y044d30,A/SouthAfrica/R14850/2021,plate11-AACTCCGCAGACACTG,0.001882,interpolated,0.001906,5.24,0.9672,0,531.4 +Y044d30,A/SouthAfrica/R14850/2021,plate11-GAGACGTACGAAATTA,0.001368,interpolated,0.001428,8.149,0.8527,0,731.1 +Y044d30,A/SouthAfrica/R14850/2021,plate11-TACTCAACAAGATAAA,0.002554,interpolated,0.002554,8.096,1,0,391.6 +Y044d30,A/SouthAfrica/R16462/2021,plate11-CACCATTAAAGAGGTA,6.664e-05,interpolated,6.704e-05,18.36,0.9471,0,1.501e+04 +Y044d30,A/SouthAfrica/R16462/2021,plate11-CGGCGTATCGTTCACA,6.515e-05,interpolated,6.557e-05,17.89,0.9456,0,1.535e+04 +Y044d30,A/SouthAfrica/R16462/2021,plate11-CTAGCAGATTGTATAA,6.297e-05,interpolated,6.335e-05,19.23,0.9453,0,1.588e+04 +Y044d30,A/Sydney/43/2022,plate11-CTATTAATCATGCAAA,0.0003616,interpolated,0.0003615,3.985,1,0,2766 +Y044d30,A/Sydney/43/2022,plate11-TACGGACATTCTTAAC,0.001014,interpolated,0.001014,5.512,1,0,986.4 +Y044d30,A/Sydney/43/2022,plate11-TAGTATAATAGAGCAG,0.0006098,interpolated,0.0006098,16.95,1,0,1640 +Y044d30,A/Togo/0274/2021,plate11-AACGAATGAATTTCTT,6.508e-05,interpolated,6.616e-05,16.83,0.8792,0,1.537e+04 +Y044d30,A/Togo/0274/2021,plate11-GTAACATTATACGATT,3.627e-05,interpolated,3.413e-05,1.536,1.049,0,2.757e+04 +Y044d30,A/Togo/0274/2021,plate11-TAGCAGATGTATCAAT,6.802e-05,interpolated,6.825e-05,3.476,0.9942,0,1.47e+04 +Y044d30,A/Togo/0304/2021,plate11-AACTCTAAAGATATAA,5.597e-05,interpolated,5.596e-05,6.863,1.001,0,1.787e+04 +Y044d30,A/Togo/0304/2021,plate11-AGAGATAATAACAAAA,0.0001083,interpolated,0.0001055,1.69,1.023,0,9236 +Y044d30,A/Togo/0304/2021,plate11-GAAGAATGGTTTTCTG,0.0001759,interpolated,0.0001759,15.2,1,0,5686 +Y044d30,A/Togo/845/2020,plate11-AGGTCAAGACCACAGG,6.216e-05,interpolated,6.227e-05,6.486,0.9943,0,1.609e+04 +Y044d30,A/Togo/845/2020,plate11-GCATGGATCCTTTACT,5.894e-05,interpolated,5.888e-05,5.105,1.003,0,1.697e+04 +Y044d30,A/Togo/845/2020,plate11-TTACCGTCTACGCATA,5.248e-05,interpolated,5.241e-05,5.429,1.004,0,1.906e+04 +Y044d30,A/Utah/27/2022,plate11-ACAATGTGACTCACCC,0.0008299,interpolated,0.0008299,8.548,1,0,1205 +Y044d30,A/Utah/27/2022,plate11-TAAATAACTCGTATTT,0.000944,interpolated,0.000944,5.339,1,0,1059 +Y044d30,A/Utah/27/2022,plate11-TCCTTGTAATTCAACT,0.0006086,interpolated,0.0006086,15.11,1,0,1643 +Y044d30,A/Washington/23/2020,plate11-ACGGAATCCCCTGAGA,0.000228,interpolated,0.0002301,15.36,0.9343,0,4387 +Y044d30,A/Washington/23/2020,plate11-GAACTGGCGTCAATCA,0.0002056,interpolated,0.0003319,2.128,0.6805,0,4864 +Y044d30,A/Washington/23/2020,plate11-GGATAAGAAAACTACT,0.001116,interpolated,0.001119,13.89,0.986,0,895.9 +Y044d30,A/Wisconsin/588/2019,plate11-AGTCCTATCCTCAAAT,0.001153,interpolated,0.001155,11.64,0.9888,0,867.4 +Y044d30,A/Wisconsin/588/2019,plate11-GAAGAAACTATAACCA,0.001236,interpolated,0.001239,9.308,0.9882,0,809 +Y044d30,A/Wisconsin/588/2019,plate11-TATATTAGTAACATAA,0.001132,interpolated,0.001133,11.66,0.9959,0,883 diff --git a/test_example/results/plates/plate2/curvefits.csv b/test_example/results/plates/plate2/curvefits.csv new file mode 100644 index 0000000..54c7b13 --- /dev/null +++ b/test_example/results/plates/plate2/curvefits.csv @@ -0,0 +1,331 @@ +serum,virus,replicate,ic50,ic50_bound,midpoint,slope,top,bottom,nt50 +M099d0,A/Bangladesh/2221/2021,plate2-AAGAGAAATATTCGCT,0.004743,interpolated,0.004743,7.447,1,0,210.8 +M099d0,A/Bangladesh/2221/2021,plate2-GACAGCAATGCATACA,0.006126,interpolated,0.006125,5.789,1,0,163.2 +M099d0,A/Bangladesh/2221/2021,plate2-GATAGAAATACCAGGA,0.004998,interpolated,0.005005,17.87,0.9883,0,200.1 +M099d0,A/Bangladesh/3210810034/2021,plate2-AACTATAGATCTAGAA,0.004987,interpolated,0.004987,8.986,1,0,200.5 +M099d0,A/Bangladesh/3210810034/2021,plate2-ACAAAAGTACCTCTAC,0.005171,interpolated,0.005176,17.21,0.9916,0,193.4 +M099d0,A/Bangladesh/8002/2021,plate2-AGTGTCCCTAAGAGGC,0.005069,interpolated,0.005098,16.6,0.9558,0,197.3 +M099d0,A/Bangladesh/8002/2021,plate2-GCAACGCCAAATAATT,0.005473,interpolated,0.005505,19.83,0.9459,0,182.7 +M099d0,A/Bangladesh/8002/2021,plate2-TCTGCTAAACTAAGTA,0.005111,interpolated,0.005137,18.46,0.9548,0,195.6 +M099d0,A/Bangladesh/8036/2021,plate2-ACGGGGCCCAGGTAAT,0.00488,interpolated,0.00488,7.843,1,0,204.9 +M099d0,A/Bangladesh/8036/2021,plate2-ATACCTCAACCTTGAA,0.004977,interpolated,0.004977,18.75,0.9986,0,200.9 +M099d0,A/Bangladesh/8036/2021,plate2-CAGTTCTGCGACCAGC,0.004149,interpolated,0.004149,9.195,1,0,241 +M099d0,A/Belgium/H0017/2022,plate2-AATGAAAGTTAGCATT,0.001805,interpolated,0.00181,3.352,0.9956,0,553.9 +M099d0,A/Belgium/H0017/2022,plate2-ATGTCCATAAAAAATA,0.002493,interpolated,0.002493,5.792,1,0,401.2 +M099d0,A/Belgium/H0017/2022,plate2-GTAAAGCAAATCCATT,0.002241,interpolated,0.002241,4.429,1.001,0,446.2 +M099d0,A/Belgium/H0038/2022,plate2-GATCCGTACTTTGATT,0.001605,interpolated,0.001605,9.152,1,0,623.2 +M099d0,A/Belgium/H0038/2022,plate2-GCCGGAGGGCATTTTC,0.0009834,interpolated,0.001025,2.536,0.9498,0,1017 +M099d0,A/Belgium/H0038/2022,plate2-TACCGTATAATTAAAA,0.002098,interpolated,0.002124,3.108,0.9818,0,476.6 +M099d0,A/Brisbane/02/2018,plate2-ACGACATGATCAAACG,0.0006658,interpolated,0.0006631,1.568,1.003,0,1502 +M099d0,A/Brisbane/02/2018,plate2-ATCCGATTTAAAGGCA,0.001515,interpolated,0.001515,9.976,1,0,660.2 +M099d0,A/Brisbane/02/2018,plate2-TAATAAGCCAGCAAGA,0.001779,interpolated,0.00178,17.22,0.9952,0,562.3 +M099d0,A/Brisbane/02/2018,plate2-TTGGGCACTAAATTAA,0.001584,interpolated,0.001584,8.013,1,0,631.5 +M099d0,A/Brisbane/48/2022,plate2-CCCTATGCTGCGTATT,0.004958,interpolated,0.004957,6.21,1,0,201.7 +M099d0,A/Brisbane/48/2022,plate2-GAGCTCTAAAGCAACA,0.004716,interpolated,0.004716,10.69,1,0,212 +M099d0,A/Brisbane/48/2022,plate2-TTATGATCTAAACAGA,0.004971,interpolated,0.004971,11.45,1,0,201.2 +M099d0,A/California/07/2009,plate2-CATGTGAATTCGCCCA,0.001639,interpolated,0.001639,7.922,1,0,610.2 +M099d0,A/California/07/2009,plate2-CCTTTCTCAAAACATA,0.0009191,interpolated,0.0009925,1.785,0.9359,0,1088 +M099d0,A/California/07/2009,plate2-CGCCTAATGTTAATAA,0.0009178,interpolated,0.0009087,1.912,1.01,0,1090 +M099d0,A/California/07/2009,plate2-GACACAGAACCCATGC,0.001479,interpolated,0.001495,3.498,0.9815,0,676.1 +M099d0,A/Chester/5355/2022,plate2-AAAAAACGCATGTAGA,0.005254,interpolated,0.005254,15.45,1,0,190.3 +M099d0,A/Chester/5355/2022,plate2-CCTCAAAATAACAAGC,0.00487,interpolated,0.00487,9.128,1,0,205.3 +M099d0,A/Chester/5355/2022,plate2-TCATATAAAGAAAAGG,0.005067,interpolated,0.005067,8.434,1,0,197.3 +M099d0,A/Cote_DIvoire/1448/2021,plate2-GTCCGTTGATAAAGAG,0.001667,interpolated,0.001667,9.818,1,0,599.9 +M099d0,A/Cote_DIvoire/1448/2021,plate2-GTTAAACGATCTATAG,0.002921,interpolated,0.002921,7.734,1,0,342.3 +M099d0,A/Cote_DIvoire/1448/2021,plate2-TCGAGAACACCCATAA,0.001689,interpolated,0.001691,17.21,0.9901,0,592.2 +M099d0,A/England/220200318/2022,plate2-CGTAATACATTTAAGA,0.001584,interpolated,0.001584,9.901,1,0,631.1 +M099d0,A/England/220200318/2022,plate2-GACCAACTGTGGTACA,0.001766,interpolated,0.001753,2.496,1.009,0,566.2 +M099d0,A/England/220200318/2022,plate2-GCTGCGCCTAACATAA,0.001745,interpolated,0.001745,6.436,1,0,572.9 +M099d0,A/Ghana/138/2020,plate2-CCAGTTCCCTTCGATG,0.001649,interpolated,0.001649,9.863,1,0,606.3 +M099d0,A/Ghana/138/2020,plate2-GACTATGGTCTAAAAA,0.001271,interpolated,0.00127,3.727,1,0,787 +M099d0,A/Ghana/138/2020,plate2-TAAGCCATAAATCAAT,0.001619,interpolated,0.001619,11.13,1,0,617.5 +M099d0,A/Ghana/2080/2020,plate2-CAGCAAAAGCATCACC,0.001892,interpolated,0.001892,17.64,0.9998,0,528.5 +M099d0,A/Ghana/2080/2020,plate2-GCAATCCCGCAATTTG,0.001117,interpolated,0.001229,2.89,0.8796,0,895.3 +M099d0,A/Ghana/2080/2020,plate2-GTAGTGCATCATTGAT,0.001531,interpolated,0.001531,6.735,1,0,653 +M099d0,A/Hawaii/70/2019,plate2-ACATGAATTCAGACGG,0.001691,interpolated,0.001691,7.687,1,0,591.3 +M099d0,A/Hawaii/70/2019,plate2-AGTAAACATGCATTGG,0.001921,interpolated,0.001922,15.52,0.9929,0,520.7 +M099d0,A/Hawaii/70/2019,plate2-ATAGAATCGCAAATTA,0.001787,interpolated,0.001787,15.13,1,0,559.6 +M099d0,A/Hawaii/70/2019,plate2-TGGAATCGTCACCGAT,0.001433,interpolated,0.001435,1.84,0.9984,0,698 +M099d0,A/India-PUN-NIV328484/2021,plate2-GATCTAATAATACGGC,0.004915,interpolated,0.004915,12.16,1,0,203.5 +M099d0,A/India-PUN-NIV328484/2021,plate2-TCTGTTCCGGCCCGAA,0.005043,interpolated,0.005072,21.12,0.9424,0,198.3 +M099d0,A/India-PUN-NIV328484/2021,plate2-TTGTCCCGAGACAACA,0.003961,interpolated,0.003958,5.745,1.002,0,252.5 +M099d0,A/India-Pune-Nivcov2221170/2022,plate2-AAATCTACCGCATTAT,0.005614,interpolated,0.005622,6.414,0.9951,0,178.1 +M099d0,A/India-Pune-Nivcov2221170/2022,plate2-CGTTTAAACAATGAAG,0.00572,interpolated,0.00572,5.316,1,0,174.8 +M099d0,A/India/Pun-NIV312851/2021,plate2-ACAGCAAATACTCACA,0.005108,interpolated,0.005137,23.59,0.9371,0,195.8 +M099d0,A/India/Pun-NIV312851/2021,plate2-CAAGAACCCAAATATA,0.004695,interpolated,0.004695,14.11,1,0,213 +M099d0,A/India/Pun-NIV312851/2021,plate2-GTAGCTATAACTAATA,0.005183,interpolated,0.005183,18.97,0.9998,0,192.9 +M099d0,A/Michigan/19/2021,plate2-AACGTTAACAAATGAA,0.005025,interpolated,0.005035,18.09,0.9832,0,199 +M099d0,A/Michigan/19/2021,plate2-AGAGAAAAAACAGTGA,0.005281,interpolated,0.005281,9.155,1,0,189.3 +M099d0,A/Michigan/19/2021,plate2-TAATGAGCTTTATGGT,0.004811,interpolated,0.004811,11.56,1,0,207.8 +M099d0,A/Michigan/45/2015,plate2-ACAAAGTCTCGAGAAG,0.001769,interpolated,0.00177,18.29,0.9988,0,565.2 +M099d0,A/Michigan/45/2015,plate2-CACCTAGGATCGCACT,0.001154,interpolated,0.001129,1.297,1.014,0,866.4 +M099d0,A/Michigan/45/2015,plate2-TGAGGATAATCACAAG,0.0009715,interpolated,0.001009,2.357,0.9568,0,1029 +M099d0,A/Michigan/45/2015,plate2-TTGAAAAAATCATAAA,0.001501,interpolated,0.0015,5.293,1.001,0,666.1 +M099d0,A/Newcastle/2/2022,plate2-CAAATATATCTTCATG,0.004984,interpolated,0.005013,17.22,0.9532,0,200.6 +M099d0,A/Newcastle/2/2022,plate2-GCCCAAGTAGGTGCAA,0.004316,interpolated,0.004315,7.244,1,0,231.7 +M099d0,A/Newcastle/2/2022,plate2-TTCACTAAGATTTCAT,0.005197,interpolated,0.005197,15.62,1,0,192.4 +M099d0,A/Niger/10217/2021,plate2-AAATAAGTACGCAAAT,0.001969,interpolated,0.001973,15.38,0.9849,0,507.8 +M099d0,A/Niger/10217/2021,plate2-CATCAACCGCCATTTC,0.0009738,interpolated,0.001089,1.84,0.9069,0,1027 +M099d0,A/Niger/10217/2021,plate2-GAACGATTGTAATTTT,0.001531,interpolated,0.001531,3.014,0.9993,0,653.2 +M099d0,A/Nimes/871/2021,plate2-ACCTTACTAAATCCTG,0.00119,interpolated,0.001188,2.347,1.002,0,840.2 +M099d0,A/Nimes/871/2021,plate2-GTTCCTTTAAGCCAAA,0.001554,interpolated,0.001554,5.931,1.001,0,643.4 +M099d0,A/Nimes/871/2021,plate2-TAATTACATTGCGGTT,0.002552,interpolated,0.002592,6.679,0.9507,0,391.9 +M099d0,A/Norway/25089/2022,plate2-CGGATAAAAATGATAT,0.004656,interpolated,0.004655,6.138,1,0,214.8 +M099d0,A/Norway/25089/2022,plate2-GACTCAATAATCACAC,0.005748,interpolated,0.005747,5.29,1,0,174 +M099d0,A/Norway/25089/2022,plate2-TGGAAAAGATGTAATA,0.00544,interpolated,0.005446,17.74,0.9897,0,183.8 +M099d0,A/Paris/30353/2021,plate2-ACATAAGAACCCTATA,0.001761,interpolated,0.00177,22.29,0.9475,0,567.7 +M099d0,A/Paris/30353/2021,plate2-ACATTTCCCTCGATAT,0.001708,interpolated,0.001713,24.44,0.9668,0,585.4 +M099d0,A/Paris/30353/2021,plate2-GTTTGACAATCACTAC,0.001299,interpolated,0.00129,1.587,1.006,0,769.6 +M099d0,A/Paris/31196/2021,plate2-AAACTAAAAGCAAGGG,0.00111,interpolated,0.001109,3.087,1.001,0,900.7 +M099d0,A/Paris/31196/2021,plate2-AATAAGTATACGGGAT,0.001067,interpolated,0.001162,3.213,0.8794,0,937.6 +M099d0,A/Paris/31196/2021,plate2-AGCAGCCTGAAAATAT,0.001446,interpolated,0.001446,4.809,1,0,691.6 +M099d0,A/Perth/1/2022,plate2-AGCCCCGTGAGAAGCA,0.004948,interpolated,0.004967,17.67,0.968,0,202.1 +M099d0,A/Perth/1/2022,plate2-CTGCACGAGAGACTTC,0.005208,interpolated,0.005209,18.93,0.9983,0,192 +M099d0,A/Perth/1/2022,plate2-TTGGGGAAATATATAA,0.00489,interpolated,0.00489,11.75,1,0,204.5 +M099d0,A/SouthAfrica/R14850/2021,plate2-AACTCCGCAGACACTG,0.003393,interpolated,0.003392,3.22,1.001,0,294.7 +M099d0,A/SouthAfrica/R14850/2021,plate2-GAGACGTACGAAATTA,0.003901,interpolated,0.003897,5.275,1.003,0,256.3 +M099d0,A/SouthAfrica/R14850/2021,plate2-TACTCAACAAGATAAA,0.004116,interpolated,0.004111,4.362,1.003,0,243 +M099d0,A/SouthAfrica/R16462/2021,plate2-CACCATTAAAGAGGTA,0.0007459,interpolated,0.0007933,2.116,0.939,0,1341 +M099d0,A/SouthAfrica/R16462/2021,plate2-CGGCGTATCGTTCACA,0.001148,interpolated,0.001145,2.261,1.003,0,871.1 +M099d0,A/SouthAfrica/R16462/2021,plate2-CTAGCAGATTGTATAA,0.003875,interpolated,0.003884,34.49,0.9645,0,258 +M099d0,A/Sydney/43/2022,plate2-CTATTAATCATGCAAA,0.004945,interpolated,0.004959,18.34,0.9755,0,202.2 +M099d0,A/Sydney/43/2022,plate2-TACGGACATTCTTAAC,0.005124,interpolated,0.00513,16.87,0.991,0,195.2 +M099d0,A/Sydney/43/2022,plate2-TAGTATAATAGAGCAG,0.003461,interpolated,0.003477,3.952,0.9909,0,289 +M099d0,A/Togo/0274/2021,plate2-AACGAATGAATTTCTT,0.001795,interpolated,0.001815,18.14,0.908,0,557.1 +M099d0,A/Togo/0274/2021,plate2-GTAACATTATACGATT,0.00142,interpolated,0.001503,2.721,0.9282,0,704.2 +M099d0,A/Togo/0274/2021,plate2-TAGCAGATGTATCAAT,0.002925,interpolated,0.002923,6.035,1.002,0,341.9 +M099d0,A/Togo/0304/2021,plate2-AACTCTAAAGATATAA,0.001235,interpolated,0.001233,2.436,1.002,0,809.8 +M099d0,A/Togo/0304/2021,plate2-AGAGATAATAACAAAA,0.0009204,interpolated,0.0009173,2.499,1.004,0,1086 +M099d0,A/Togo/0304/2021,plate2-GAAGAATGGTTTTCTG,0.001763,interpolated,0.001763,15.34,1,0,567.2 +M099d0,A/Togo/845/2020,plate2-AGGTCAAGACCACAGG,0.001499,interpolated,0.00154,2.919,0.9625,0,667 +M099d0,A/Togo/845/2020,plate2-GCATGGATCCTTTACT,0.001672,interpolated,0.001677,17.01,0.9773,0,598.1 +M099d0,A/Togo/845/2020,plate2-TTACCGTCTACGCATA,0.001487,interpolated,0.001486,5.289,1.001,0,672.6 +M099d0,A/Utah/27/2022,plate2-ACAATGTGACTCACCC,0.005001,interpolated,0.005001,11.49,1,0,200 +M099d0,A/Utah/27/2022,plate2-TAAATAACTCGTATTT,0.005076,interpolated,0.005076,19,0.9996,0,197 +M099d0,A/Utah/27/2022,plate2-TCCTTGTAATTCAACT,0.005075,interpolated,0.005078,18.56,0.9947,0,197 +M099d0,A/Washington/23/2020,plate2-ACGGAATCCCCTGAGA,0.003042,interpolated,0.003041,3.42,1.001,0,328.7 +M099d0,A/Washington/23/2020,plate2-GAACTGGCGTCAATCA,0.004694,interpolated,0.004694,12.72,1,0,213 +M099d0,A/Washington/23/2020,plate2-GGATAAGAAAACTACT,0.004726,interpolated,0.004726,16,1,0,211.6 +M099d0,A/Wisconsin/588/2019,plate2-AGTCCTATCCTCAAAT,0.005155,interpolated,0.005194,25.08,0.9135,0,194 +M099d0,A/Wisconsin/588/2019,plate2-GAAGAAACTATAACCA,0.003685,interpolated,0.0037,7.581,0.9852,0,271.3 +M099d0,A/Wisconsin/588/2019,plate2-TATATTAGTAACATAA,0.005262,interpolated,0.005262,19.15,0.9997,0,190 +M099d30,A/Bangladesh/2221/2021,plate2-AAGAGAAATATTCGCT,0.0005983,interpolated,0.0006347,2.522,0.9308,0,1671 +M099d30,A/Bangladesh/2221/2021,plate2-GACAGCAATGCATACA,0.0007165,interpolated,0.0007164,5.063,1,0,1396 +M099d30,A/Bangladesh/2221/2021,plate2-GATAGAAATACCAGGA,0.0009284,interpolated,0.0009328,11.16,0.9741,0,1077 +M099d30,A/Bangladesh/3210810034/2021,plate2-AACTATAGATCTAGAA,0.0006375,interpolated,0.0006373,4.856,1.001,0,1569 +M099d30,A/Bangladesh/3210810034/2021,plate2-ACAAAAGTACCTCTAC,0.000728,interpolated,0.0007279,4.741,1,0,1374 +M099d30,A/Bangladesh/8002/2021,plate2-AGTGTCCCTAAGAGGC,0.001484,interpolated,0.001499,26.55,0.8792,0,674 +M099d30,A/Bangladesh/8002/2021,plate2-GCAACGCCAAATAATT,0.0005196,interpolated,0.0005779,3.857,0.8317,0,1925 +M099d30,A/Bangladesh/8002/2021,plate2-TCTGCTAAACTAAGTA,0.0005865,interpolated,0.0005897,15.69,0.9579,0,1705 +M099d30,A/Bangladesh/8036/2021,plate2-ACGGGGCCCAGGTAAT,0.0005879,interpolated,0.0005879,8.601,1,0,1701 +M099d30,A/Bangladesh/8036/2021,plate2-ATACCTCAACCTTGAA,0.0005966,interpolated,0.0006021,17.33,0.9265,0,1676 +M099d30,A/Bangladesh/8036/2021,plate2-CAGTTCTGCGACCAGC,0.0006125,interpolated,0.0006255,16.32,0.8555,0,1633 +M099d30,A/Belgium/H0017/2022,plate2-AATGAAAGTTAGCATT,0.0002588,interpolated,0.0002581,3.067,1.004,0,3864 +M099d30,A/Belgium/H0017/2022,plate2-ATGTCCATAAAAAATA,0.0002198,interpolated,0.0002191,3.038,1.005,0,4550 +M099d30,A/Belgium/H0017/2022,plate2-GTAAAGCAAATCCATT,0.000317,interpolated,0.0003169,4.178,1,0,3155 +M099d30,A/Belgium/H0038/2022,plate2-GATCCGTACTTTGATT,0.0003135,interpolated,0.0003133,3.613,1.001,0,3190 +M099d30,A/Belgium/H0038/2022,plate2-GCCGGAGGGCATTTTC,0.0001901,interpolated,0.0001897,3.989,1.004,0,5260 +M099d30,A/Belgium/H0038/2022,plate2-TACCGTATAATTAAAA,0.0002534,interpolated,0.0002531,3.469,1.003,0,3946 +M099d30,A/Brisbane/02/2018,plate2-ACGACATGATCAAACG,8.594e-05,interpolated,7.822e-05,1.227,1.061,0,1.164e+04 +M099d30,A/Brisbane/02/2018,plate2-ATCCGATTTAAAGGCA,0.0001751,interpolated,0.000175,5.073,1.002,0,5710 +M099d30,A/Brisbane/02/2018,plate2-TAATAAGCCAGCAAGA,0.0001817,interpolated,0.0001807,3.36,1.009,0,5505 +M099d30,A/Brisbane/02/2018,plate2-TTGGGCACTAAATTAA,0.0002423,interpolated,0.00024,2.365,1.011,0,4127 +M099d30,A/Brisbane/48/2022,plate2-CCCTATGCTGCGTATT,0.0007573,interpolated,0.0007576,7.518,0.9985,0,1320 +M099d30,A/Brisbane/48/2022,plate2-GAGCTCTAAAGCAACA,0.0007266,interpolated,0.0007384,4.83,0.9627,0,1376 +M099d30,A/Brisbane/48/2022,plate2-TTATGATCTAAACAGA,0.0005899,interpolated,0.0005943,17.16,0.9398,0,1695 +M099d30,A/California/07/2009,plate2-CATGTGAATTCGCCCA,0.0001869,interpolated,0.0001869,5.438,1.001,0,5349 +M099d30,A/California/07/2009,plate2-CCTTTCTCAAAACATA,9.768e-05,interpolated,0.0001086,2.212,0.8958,0,1.024e+04 +M099d30,A/California/07/2009,plate2-CGCCTAATGTTAATAA,0.0002224,interpolated,0.0002273,2.232,0.9761,0,4497 +M099d30,A/California/07/2009,plate2-GACACAGAACCCATGC,0.0002056,interpolated,0.0002065,19.03,0.9592,0,4863 +M099d30,A/Chester/5355/2022,plate2-AAAAAACGCATGTAGA,0.0007349,interpolated,0.0007416,4.066,0.9818,0,1361 +M099d30,A/Chester/5355/2022,plate2-CCTCAAAATAACAAGC,0.0007009,interpolated,0.0007052,3.926,0.988,0,1427 +M099d30,A/Chester/5355/2022,plate2-TCATATAAAGAAAAGG,0.0007089,interpolated,0.0007089,6.88,1,0,1411 +M099d30,A/Cote_DIvoire/1448/2021,plate2-GTCCGTTGATAAAGAG,0.0002239,interpolated,0.0002302,2.805,0.9626,0,4466 +M099d30,A/Cote_DIvoire/1448/2021,plate2-GTTAAACGATCTATAG,0.0002823,interpolated,0.0002903,4.062,0.9459,0,3543 +M099d30,A/Cote_DIvoire/1448/2021,plate2-TCGAGAACACCCATAA,0.0002791,interpolated,0.0002773,1.994,1.006,0,3583 +M099d30,A/England/220200318/2022,plate2-CGTAATACATTTAAGA,0.0002354,interpolated,0.000239,2.554,0.9814,0,4247 +M099d30,A/England/220200318/2022,plate2-GACCAACTGTGGTACA,0.000292,interpolated,0.0002964,4.345,0.9689,0,3424 +M099d30,A/England/220200318/2022,plate2-GCTGCGCCTAACATAA,0.0002039,interpolated,0.0002178,3.48,0.8978,0,4904 +M099d30,A/Ghana/138/2020,plate2-CCAGTTCCCTTCGATG,0.0005145,interpolated,0.0005145,13.22,1,0,1944 +M099d30,A/Ghana/138/2020,plate2-GACTATGGTCTAAAAA,0.000523,interpolated,0.000523,13.62,1,0,1912 +M099d30,A/Ghana/138/2020,plate2-TAAGCCATAAATCAAT,0.0002299,interpolated,0.0002301,2.207,0.9992,0,4349 +M099d30,A/Ghana/2080/2020,plate2-CAGCAAAAGCATCACC,0.0003674,interpolated,0.0003674,6.346,1,0,2722 +M099d30,A/Ghana/2080/2020,plate2-GCAATCCCGCAATTTG,0.0001837,interpolated,0.000193,16.16,0.7259,0,5444 +M099d30,A/Ghana/2080/2020,plate2-GTAGTGCATCATTGAT,0.0002015,interpolated,0.0002041,19.17,0.8898,0,4963 +M099d30,A/Hawaii/70/2019,plate2-ACATGAATTCAGACGG,0.00034,interpolated,0.0003454,4.69,0.9641,0,2941 +M099d30,A/Hawaii/70/2019,plate2-AGTAAACATGCATTGG,0.0003025,interpolated,0.0003324,3.616,0.8555,0,3306 +M099d30,A/Hawaii/70/2019,plate2-ATAGAATCGCAAATTA,0.0002052,interpolated,0.0002131,3.193,0.9435,0,4872 +M099d30,A/Hawaii/70/2019,plate2-TGGAATCGTCACCGAT,0.0002134,interpolated,0.000221,3.567,0.9414,0,4685 +M099d30,A/India-PUN-NIV328484/2021,plate2-GATCTAATAATACGGC,0.0006463,interpolated,0.0006527,13.48,0.9379,0,1547 +M099d30,A/India-PUN-NIV328484/2021,plate2-TCTGTTCCGGCCCGAA,0.0003173,interpolated,0.0003432,2.862,0.8993,0,3152 +M099d30,A/India-PUN-NIV328484/2021,plate2-TTGTCCCGAGACAACA,0.0004707,interpolated,0.0004707,3.756,1,0,2124 +M099d30,A/India-Pune-Nivcov2221170/2022,plate2-AAATCTACCGCATTAT,0.001002,interpolated,0.001011,5.643,0.9754,0,998.2 +M099d30,A/India-Pune-Nivcov2221170/2022,plate2-CGTTTAAACAATGAAG,0.0009699,interpolated,0.0009717,4.747,0.9956,0,1031 +M099d30,A/India/Pun-NIV312851/2021,plate2-ACAGCAAATACTCACA,0.0003731,interpolated,0.0004645,2.275,0.8037,0,2680 +M099d30,A/India/Pun-NIV312851/2021,plate2-CAAGAACCCAAATATA,0.0005496,interpolated,0.0005496,6.685,1,0,1819 +M099d30,A/India/Pun-NIV312851/2021,plate2-GTAGCTATAACTAATA,0.001724,interpolated,0.00173,17.65,0.9668,0,580.2 +M099d30,A/Michigan/19/2021,plate2-AACGTTAACAAATGAA,0.0005822,interpolated,0.000585,16.7,0.9613,0,1718 +M099d30,A/Michigan/19/2021,plate2-AGAGAAAAAACAGTGA,0.0005689,interpolated,0.0005993,3.945,0.9073,0,1758 +M099d30,A/Michigan/19/2021,plate2-TAATGAGCTTTATGGT,0.0005814,interpolated,0.0005814,7.473,1,0,1720 +M099d30,A/Michigan/45/2015,plate2-ACAAAGTCTCGAGAAG,0.0002221,interpolated,0.0002143,1.619,1.03,0,4503 +M099d30,A/Michigan/45/2015,plate2-CACCTAGGATCGCACT,0.0002019,interpolated,0.0002037,17.77,0.9252,0,4953 +M099d30,A/Michigan/45/2015,plate2-TGAGGATAATCACAAG,0.0001231,interpolated,0.000123,3.45,1.001,0,8125 +M099d30,A/Michigan/45/2015,plate2-TTGAAAAAATCATAAA,0.0001841,interpolated,0.0001838,3.869,1.003,0,5432 +M099d30,A/Newcastle/2/2022,plate2-CAAATATATCTTCATG,0.0004632,interpolated,0.0005279,1.821,0.8941,0,2159 +M099d30,A/Newcastle/2/2022,plate2-GCCCAAGTAGGTGCAA,0.001294,interpolated,0.001294,21.62,1,0,772.9 +M099d30,A/Newcastle/2/2022,plate2-TTCACTAAGATTTCAT,0.0005615,interpolated,0.0005614,7.47,1,0,1781 +M099d30,A/Niger/10217/2021,plate2-AAATAAGTACGCAAAT,0.0004175,interpolated,0.0004175,4.548,1,0,2395 +M099d30,A/Niger/10217/2021,plate2-CATCAACCGCCATTTC,0.0005712,interpolated,0.0005806,17.53,0.8754,0,1751 +M099d30,A/Niger/10217/2021,plate2-GAACGATTGTAATTTT,0.0005414,interpolated,0.0005432,19.93,0.9682,0,1847 +M099d30,A/Nimes/871/2021,plate2-ACCTTACTAAATCCTG,0.0002871,interpolated,0.000283,1.809,1.013,0,3483 +M099d30,A/Nimes/871/2021,plate2-GTTCCTTTAAGCCAAA,0.0005607,interpolated,0.0005616,17.54,0.9864,0,1784 +M099d30,A/Nimes/871/2021,plate2-TAATTACATTGCGGTT,0.0002312,interpolated,0.0002308,3.672,1.003,0,4326 +M099d30,A/Norway/25089/2022,plate2-CGGATAAAAATGATAT,0.001479,interpolated,0.001479,16.01,1,0,675.9 +M099d30,A/Norway/25089/2022,plate2-GACTCAATAATCACAC,0.001623,interpolated,0.001628,18,0.9739,0,616.2 +M099d30,A/Norway/25089/2022,plate2-TGGAAAAGATGTAATA,0.0007571,interpolated,0.000782,3.093,0.9523,0,1321 +M099d30,A/Paris/30353/2021,plate2-ACATAAGAACCCTATA,0.0003244,interpolated,0.0003233,2.524,1.005,0,3082 +M099d30,A/Paris/30353/2021,plate2-ACATTTCCCTCGATAT,0.0006111,interpolated,0.000616,20.46,0.925,0,1636 +M099d30,A/Paris/30353/2021,plate2-GTTTGACAATCACTAC,0.0002959,interpolated,0.0003033,3.82,0.9545,0,3380 +M099d30,A/Paris/31196/2021,plate2-AAACTAAAAGCAAGGG,0.0002975,interpolated,0.0003046,2.591,0.9705,0,3361 +M099d30,A/Paris/31196/2021,plate2-AATAAGTATACGGGAT,0.0001901,interpolated,0.000224,3.452,0.7839,0,5259 +M099d30,A/Paris/31196/2021,plate2-AGCAGCCTGAAAATAT,0.0003087,interpolated,0.0003084,3.236,1.002,0,3239 +M099d30,A/Perth/1/2022,plate2-AGCCCCGTGAGAAGCA,0.0005468,interpolated,0.0005798,2.734,0.926,0,1829 +M099d30,A/Perth/1/2022,plate2-CTGCACGAGAGACTTC,0.0005527,interpolated,0.0005527,6.424,1,0,1809 +M099d30,A/Perth/1/2022,plate2-TTGGGGAAATATATAA,0.0003886,interpolated,0.0004431,2.017,0.8835,0,2574 +M099d30,A/SouthAfrica/R14850/2021,plate2-AACTCCGCAGACACTG,0.000666,interpolated,0.0006938,4.756,0.9117,0,1501 +M099d30,A/SouthAfrica/R14850/2021,plate2-GAGACGTACGAAATTA,0.0008463,interpolated,0.0008446,2.928,1.003,0,1182 +M099d30,A/SouthAfrica/R14850/2021,plate2-TACTCAACAAGATAAA,0.0008017,interpolated,0.0007922,1.95,1.012,0,1247 +M099d30,A/SouthAfrica/R16462/2021,plate2-CACCATTAAAGAGGTA,0.0002456,interpolated,0.0003,4.085,0.721,0,4071 +M099d30,A/SouthAfrica/R16462/2021,plate2-CGGCGTATCGTTCACA,0.0002866,interpolated,0.0002894,2.219,0.9894,0,3490 +M099d30,A/SouthAfrica/R16462/2021,plate2-CTAGCAGATTGTATAA,0.0005267,interpolated,0.0005267,12.32,1,0,1899 +M099d30,A/Sydney/43/2022,plate2-CTATTAATCATGCAAA,0.0008971,interpolated,0.0009237,7.483,0.9019,0,1115 +M099d30,A/Sydney/43/2022,plate2-TACGGACATTCTTAAC,0.0006312,interpolated,0.0006321,3.712,0.9975,0,1584 +M099d30,A/Sydney/43/2022,plate2-TAGTATAATAGAGCAG,0.0003237,interpolated,0.0003677,2.097,0.8829,0,3089 +M099d30,A/Togo/0274/2021,plate2-AACGAATGAATTTCTT,0.0002749,interpolated,0.0002987,2.717,0.8991,0,3637 +M099d30,A/Togo/0274/2021,plate2-GTAACATTATACGATT,0.0003593,interpolated,0.0003693,3.13,0.9589,0,2783 +M099d30,A/Togo/0274/2021,plate2-TAGCAGATGTATCAAT,0.0002879,interpolated,0.0002838,1.734,1.013,0,3473 +M099d30,A/Togo/0304/2021,plate2-AACTCTAAAGATATAA,0.0006618,interpolated,0.0006618,15.44,1,0,1511 +M099d30,A/Togo/0304/2021,plate2-AGAGATAATAACAAAA,0.0002412,interpolated,0.000256,2.174,0.9392,0,4146 +M099d30,A/Togo/0304/2021,plate2-GAAGAATGGTTTTCTG,0.0002519,interpolated,0.0002635,2.356,0.9499,0,3969 +M099d30,A/Togo/845/2020,plate2-AGGTCAAGACCACAGG,0.000454,interpolated,0.0004474,1.305,1.01,0,2203 +M099d30,A/Togo/845/2020,plate2-GCATGGATCCTTTACT,0.0003926,interpolated,0.000394,2.568,0.9953,0,2547 +M099d30,A/Togo/845/2020,plate2-TTACCGTCTACGCATA,0.0003953,interpolated,0.0004059,3.379,0.9571,0,2530 +M099d30,A/Utah/27/2022,plate2-ACAATGTGACTCACCC,0.0006583,interpolated,0.0006582,4.067,1,0,1519 +M099d30,A/Utah/27/2022,plate2-TAAATAACTCGTATTT,0.0006263,interpolated,0.0006263,7.423,1,0,1597 +M099d30,A/Utah/27/2022,plate2-TCCTTGTAATTCAACT,0.0004975,interpolated,0.0005011,3.924,0.986,0,2010 +M099d30,A/Washington/23/2020,plate2-ACGGAATCCCCTGAGA,0.0002612,interpolated,0.0002692,3.86,0.9453,0,3828 +M099d30,A/Washington/23/2020,plate2-GAACTGGCGTCAATCA,0.0003208,interpolated,0.0003184,2.154,1.008,0,3117 +M099d30,A/Washington/23/2020,plate2-GGATAAGAAAACTACT,0.0003255,interpolated,0.0003255,4.897,1,0,3072 +M099d30,A/Wisconsin/588/2019,plate2-AGTCCTATCCTCAAAT,0.0005445,interpolated,0.0005572,23.94,0.7871,0,1837 +M099d30,A/Wisconsin/588/2019,plate2-GAAGAAACTATAACCA,0.0002298,interpolated,0.0002601,3.463,0.8254,0,4352 +M099d30,A/Wisconsin/588/2019,plate2-TATATTAGTAACATAA,0.0002193,interpolated,0.0002291,2.449,0.9492,0,4560 +Y154d182,A/Bangladesh/2221/2021,plate2-AAGAGAAATATTCGCT,0.005053,interpolated,0.00508,23.87,0.939,0,197.9 +Y154d182,A/Bangladesh/2221/2021,plate2-GACAGCAATGCATACA,0.005249,interpolated,0.005249,6.964,1,0,190.5 +Y154d182,A/Bangladesh/2221/2021,plate2-GATAGAAATACCAGGA,0.005227,interpolated,0.005225,4.935,1.001,0,191.3 +Y154d182,A/Bangladesh/3210810034/2021,plate2-AACTATAGATCTAGAA,0.005166,interpolated,0.005166,15.71,1,0,193.6 +Y154d182,A/Bangladesh/3210810034/2021,plate2-ACAAAAGTACCTCTAC,0.004804,interpolated,0.004804,12.68,1,0,208.2 +Y154d182,A/Bangladesh/8002/2021,plate2-AGTGTCCCTAAGAGGC,0.005072,interpolated,0.005117,21.56,0.914,0,197.2 +Y154d182,A/Bangladesh/8002/2021,plate2-GCAACGCCAAATAATT,0.004927,interpolated,0.00496,21.66,0.9321,0,203 +Y154d182,A/Bangladesh/8002/2021,plate2-TCTGCTAAACTAAGTA,0.004562,interpolated,0.004562,15.99,1,0,219.2 +Y154d182,A/Bangladesh/8036/2021,plate2-ACGGGGCCCAGGTAAT,0.004793,interpolated,0.004793,12.69,1,0,208.6 +Y154d182,A/Bangladesh/8036/2021,plate2-ATACCTCAACCTTGAA,0.005205,interpolated,0.005223,18.24,0.968,0,192.1 +Y154d182,A/Bangladesh/8036/2021,plate2-CAGTTCTGCGACCAGC,0.004171,interpolated,0.004171,11.35,1,0,239.8 +Y154d182,A/Belgium/H0017/2022,plate2-AATGAAAGTTAGCATT,0.0003221,interpolated,0.0003227,3.719,0.9966,0,3104 +Y154d182,A/Belgium/H0017/2022,plate2-ATGTCCATAAAAAATA,0.0007404,interpolated,0.0007465,7.81,0.9689,0,1351 +Y154d182,A/Belgium/H0017/2022,plate2-GTAAAGCAAATCCATT,0.0005825,interpolated,0.0005825,15.5,1,0,1717 +Y154d182,A/Belgium/H0038/2022,plate2-GATCCGTACTTTGATT,0.0003886,interpolated,0.0003884,3.228,1.001,0,2574 +Y154d182,A/Belgium/H0038/2022,plate2-GCCGGAGGGCATTTTC,0.0002672,interpolated,0.0002751,2.005,0.9718,0,3742 +Y154d182,A/Belgium/H0038/2022,plate2-TACCGTATAATTAAAA,0.0003313,interpolated,0.0003341,3.794,0.9841,0,3018 +Y154d182,A/Brisbane/02/2018,plate2-ACGACATGATCAAACG,0.0002009,interpolated,0.0002066,2.934,0.9604,0,4977 +Y154d182,A/Brisbane/02/2018,plate2-ATCCGATTTAAAGGCA,0.0003331,interpolated,0.0003423,2.454,0.9676,0,3002 +Y154d182,A/Brisbane/02/2018,plate2-TAATAAGCCAGCAAGA,0.000298,interpolated,0.0002972,2.828,1.004,0,3356 +Y154d182,A/Brisbane/02/2018,plate2-TTGGGCACTAAATTAA,0.0002372,interpolated,0.0002418,2.443,0.977,0,4216 +Y154d182,A/Brisbane/48/2022,plate2-CCCTATGCTGCGTATT,0.004823,interpolated,0.004823,12.15,1,0,207.4 +Y154d182,A/Brisbane/48/2022,plate2-GAGCTCTAAAGCAACA,0.005028,interpolated,0.005068,21.03,0.9231,0,198.9 +Y154d182,A/Brisbane/48/2022,plate2-TTATGATCTAAACAGA,0.005159,interpolated,0.005167,17.15,0.9862,0,193.8 +Y154d182,A/California/07/2009,plate2-CATGTGAATTCGCCCA,0.0004812,interpolated,0.0004812,17.27,1,0,2078 +Y154d182,A/California/07/2009,plate2-CCTTTCTCAAAACATA,0.0002028,interpolated,0.0002035,20.78,0.9683,0,4930 +Y154d182,A/California/07/2009,plate2-CGCCTAATGTTAATAA,0.0002835,interpolated,0.0002853,2.598,0.9922,0,3527 +Y154d182,A/California/07/2009,plate2-GACACAGAACCCATGC,0.0002141,interpolated,0.0002175,1.92,0.9852,0,4670 +Y154d182,A/Chester/5355/2022,plate2-AAAAAACGCATGTAGA,0.004659,interpolated,0.004659,14.31,1,0,214.6 +Y154d182,A/Chester/5355/2022,plate2-CCTCAAAATAACAAGC,0.005264,interpolated,0.005264,6.839,1,0,190 +Y154d182,A/Chester/5355/2022,plate2-TCATATAAAGAAAAGG,0.004959,interpolated,0.004959,11.22,1,0,201.6 +Y154d182,A/Cote_DIvoire/1448/2021,plate2-GTCCGTTGATAAAGAG,0.0003201,interpolated,0.000323,4.414,0.9803,0,3124 +Y154d182,A/Cote_DIvoire/1448/2021,plate2-GTTAAACGATCTATAG,0.0002813,interpolated,0.0002947,3.947,0.9161,0,3555 +Y154d182,A/Cote_DIvoire/1448/2021,plate2-TCGAGAACACCCATAA,0.0005483,interpolated,0.0005495,18.88,0.9786,0,1824 +Y154d182,A/England/220200318/2022,plate2-CGTAATACATTTAAGA,0.000398,interpolated,0.0003964,2.146,1.004,0,2513 +Y154d182,A/England/220200318/2022,plate2-GACCAACTGTGGTACA,0.0005796,interpolated,0.0005796,15.58,1,0,1725 +Y154d182,A/England/220200318/2022,plate2-GCTGCGCCTAACATAA,0.0002507,interpolated,0.0003517,1.296,0.8224,0,3988 +Y154d182,A/Ghana/138/2020,plate2-CCAGTTCCCTTCGATG,0.0003579,interpolated,0.0003579,4.942,1,0,2794 +Y154d182,A/Ghana/138/2020,plate2-GACTATGGTCTAAAAA,0.0003833,interpolated,0.0003833,5.312,1,0,2609 +Y154d182,A/Ghana/138/2020,plate2-TAAGCCATAAATCAAT,0.0002802,interpolated,0.0002844,4.242,0.9692,0,3569 +Y154d182,A/Ghana/2080/2020,plate2-CAGCAAAAGCATCACC,0.0005784,interpolated,0.0005788,18.06,0.9937,0,1729 +Y154d182,A/Ghana/2080/2020,plate2-GCAATCCCGCAATTTG,0.0002481,interpolated,0.0003628,1.407,0.793,0,4030 +Y154d182,A/Ghana/2080/2020,plate2-GTAGTGCATCATTGAT,0.0003621,interpolated,0.0003723,2.908,0.9613,0,2762 +Y154d182,A/Hawaii/70/2019,plate2-ACATGAATTCAGACGG,0.0002533,interpolated,0.0002501,2.127,1.014,0,3948 +Y154d182,A/Hawaii/70/2019,plate2-AGTAAACATGCATTGG,0.0005318,interpolated,0.0005421,21.97,0.8273,0,1880 +Y154d182,A/Hawaii/70/2019,plate2-ATAGAATCGCAAATTA,0.000294,interpolated,0.0002981,3.843,0.9737,0,3402 +Y154d182,A/Hawaii/70/2019,plate2-TGGAATCGTCACCGAT,0.0002493,interpolated,0.0002547,2.545,0.9732,0,4012 +Y154d182,A/India-PUN-NIV328484/2021,plate2-GATCTAATAATACGGC,0.004176,interpolated,0.004176,3.98,1,0,239.5 +Y154d182,A/India-PUN-NIV328484/2021,plate2-TCTGTTCCGGCCCGAA,0.004931,interpolated,0.004964,21.61,0.9321,0,202.8 +Y154d182,A/India-PUN-NIV328484/2021,plate2-TTGTCCCGAGACAACA,0.002961,interpolated,0.003007,3.082,0.9768,0,337.8 +Y154d182,A/India-Pune-Nivcov2221170/2022,plate2-AAATCTACCGCATTAT,0.005921,interpolated,0.005921,5.548,1,0,168.9 +Y154d182,A/India-Pune-Nivcov2221170/2022,plate2-CGTTTAAACAATGAAG,0.005829,interpolated,0.005834,17.15,0.993,0,171.5 +Y154d182,A/India/Pun-NIV312851/2021,plate2-ACAGCAAATACTCACA,0.004754,interpolated,0.004772,18.18,0.9663,0,210.3 +Y154d182,A/India/Pun-NIV312851/2021,plate2-CAAGAACCCAAATATA,0.004571,interpolated,0.004571,7.832,1,0,218.8 +Y154d182,A/India/Pun-NIV312851/2021,plate2-GTAGCTATAACTAATA,0.002245,interpolated,0.002264,3.16,0.987,0,445.3 +Y154d182,A/Michigan/19/2021,plate2-AACGTTAACAAATGAA,0.009601,interpolated,0.0096,10.17,1,0,104.2 +Y154d182,A/Michigan/19/2021,plate2-AGAGAAAAAACAGTGA,0.002829,interpolated,0.002864,3.514,0.9788,0,353.5 +Y154d182,A/Michigan/19/2021,plate2-TAATGAGCTTTATGGT,0.004787,interpolated,0.004787,10.43,1,0,208.9 +Y154d182,A/Michigan/45/2015,plate2-ACAAAGTCTCGAGAAG,0.0001751,interpolated,0.0001775,2.622,0.9829,0,5710 +Y154d182,A/Michigan/45/2015,plate2-CACCTAGGATCGCACT,0.0001836,interpolated,0.0001825,2.087,1.006,0,5446 +Y154d182,A/Michigan/45/2015,plate2-TGAGGATAATCACAAG,0.0001035,interpolated,0.0001056,1.157,0.9884,0,9666 +Y154d182,A/Michigan/45/2015,plate2-TTGAAAAAATCATAAA,0.0002373,interpolated,0.0002401,3.551,0.9795,0,4214 +Y154d182,A/Newcastle/2/2022,plate2-CAAATATATCTTCATG,0.003112,interpolated,0.003109,2.854,1.002,0,321.4 +Y154d182,A/Newcastle/2/2022,plate2-GCCCAAGTAGGTGCAA,0.004638,interpolated,0.004638,12.16,1,0,215.6 +Y154d182,A/Newcastle/2/2022,plate2-TTCACTAAGATTTCAT,0.00525,interpolated,0.00525,8.078,1,0,190.5 +Y154d182,A/Niger/10217/2021,plate2-AAATAAGTACGCAAAT,0.0003404,interpolated,0.0003469,3.043,0.9719,0,2938 +Y154d182,A/Niger/10217/2021,plate2-CATCAACCGCCATTTC,0.0005296,interpolated,0.0005348,18.89,0.9153,0,1888 +Y154d182,A/Niger/10217/2021,plate2-GAACGATTGTAATTTT,0.0003032,interpolated,0.0003174,2.75,0.9409,0,3298 +Y154d182,A/Nimes/871/2021,plate2-ACCTTACTAAATCCTG,0.0002906,interpolated,0.0002899,2.895,1.004,0,3441 +Y154d182,A/Nimes/871/2021,plate2-GTTCCTTTAAGCCAAA,0.0004105,interpolated,0.0004105,5.238,1,0,2436 +Y154d182,A/Nimes/871/2021,plate2-TAATTACATTGCGGTT,0.000227,interpolated,0.0002267,1.247,1.001,0,4406 +Y154d182,A/Norway/25089/2022,plate2-CGGATAAAAATGATAT,0.005302,interpolated,0.005315,16.35,0.9805,0,188.6 +Y154d182,A/Norway/25089/2022,plate2-GACTCAATAATCACAC,0.00523,interpolated,0.00523,8.372,1,0,191.2 +Y154d182,A/Norway/25089/2022,plate2-TGGAAAAGATGTAATA,0.00256,interpolated,0.002567,1.646,0.9976,0,390.6 +Y154d182,A/Paris/30353/2021,plate2-ACATAAGAACCCTATA,0.0005795,interpolated,0.0005957,4.79,0.9383,0,1726 +Y154d182,A/Paris/30353/2021,plate2-ACATTTCCCTCGATAT,0.0003586,interpolated,0.0004247,2.923,0.8048,0,2789 +Y154d182,A/Paris/30353/2021,plate2-GTTTGACAATCACTAC,0.0004336,interpolated,0.0004335,6.896,1.001,0,2306 +Y154d182,A/Paris/31196/2021,plate2-AAACTAAAAGCAAGGG,0.0001783,interpolated,0.0001999,1.598,0.9165,0,5608 +Y154d182,A/Paris/31196/2021,plate2-AATAAGTATACGGGAT,0.0001287,interpolated,0.0001365,1.551,0.9565,0,7768 +Y154d182,A/Paris/31196/2021,plate2-AGCAGCCTGAAAATAT,0.0005289,interpolated,0.0005289,21.32,0.9995,0,1891 +Y154d182,A/Perth/1/2022,plate2-AGCCCCGTGAGAAGCA,0.004891,interpolated,0.004898,18.02,0.9865,0,204.5 +Y154d182,A/Perth/1/2022,plate2-CTGCACGAGAGACTTC,0.003855,interpolated,0.003855,9.02,1,0,259.4 +Y154d182,A/Perth/1/2022,plate2-TTGGGGAAATATATAA,0.003465,interpolated,0.003465,5.662,1,0,288.6 +Y154d182,A/SouthAfrica/R14850/2021,plate2-AACTCCGCAGACACTG,0.004996,interpolated,0.005043,22.22,0.9056,0,200.2 +Y154d182,A/SouthAfrica/R14850/2021,plate2-GAGACGTACGAAATTA,0.005385,interpolated,0.005386,15.89,0.9986,0,185.7 +Y154d182,A/SouthAfrica/R14850/2021,plate2-TACTCAACAAGATAAA,0.00493,interpolated,0.00493,9.884,1,0,202.8 +Y154d182,A/SouthAfrica/R16462/2021,plate2-CACCATTAAAGAGGTA,0.0001892,interpolated,0.0002977,3.806,0.589,0,5285 +Y154d182,A/SouthAfrica/R16462/2021,plate2-CGGCGTATCGTTCACA,0.0003125,interpolated,0.0003183,2.445,0.9781,0,3200 +Y154d182,A/SouthAfrica/R16462/2021,plate2-CTAGCAGATTGTATAA,0.0003667,interpolated,0.0003665,3.3,1.001,0,2727 +Y154d182,A/Sydney/43/2022,plate2-CTATTAATCATGCAAA,0.005048,interpolated,0.005061,18.04,0.9765,0,198.1 +Y154d182,A/Sydney/43/2022,plate2-TACGGACATTCTTAAC,0.004203,interpolated,0.004202,5.693,1.001,0,237.9 +Y154d182,A/Sydney/43/2022,plate2-TAGTATAATAGAGCAG,0.002842,interpolated,0.002939,3.026,0.9517,0,351.9 +Y154d182,A/Togo/0274/2021,plate2-AACGAATGAATTTCTT,0.0002687,interpolated,0.0002788,2.464,0.9566,0,3721 +Y154d182,A/Togo/0274/2021,plate2-GTAACATTATACGATT,0.0005528,interpolated,0.0005559,21.46,0.9427,0,1809 +Y154d182,A/Togo/0274/2021,plate2-TAGCAGATGTATCAAT,0.0002879,interpolated,0.0002864,2.497,1.006,0,3474 +Y154d182,A/Togo/0304/2021,plate2-AACTCTAAAGATATAA,0.0003843,interpolated,0.0003843,5.471,1,0,2602 +Y154d182,A/Togo/0304/2021,plate2-AGAGATAATAACAAAA,0.0002379,interpolated,0.0002475,4.253,0.9227,0,4203 +Y154d182,A/Togo/0304/2021,plate2-GAAGAATGGTTTTCTG,0.0004735,interpolated,0.0004735,6.621,1,0,2112 +Y154d182,A/Togo/845/2020,plate2-AGGTCAAGACCACAGG,0.0004174,interpolated,0.0004255,4.837,0.9558,0,2396 +Y154d182,A/Togo/845/2020,plate2-GCATGGATCCTTTACT,0.0006725,interpolated,0.0007089,5.915,0.8661,0,1487 +Y154d182,A/Togo/845/2020,plate2-TTACCGTCTACGCATA,0.000551,interpolated,0.000551,15.35,1,0,1815 +Y154d182,A/Utah/27/2022,plate2-ACAATGTGACTCACCC,0.004234,interpolated,0.004234,7.938,1,0,236.2 +Y154d182,A/Utah/27/2022,plate2-TAAATAACTCGTATTT,0.003633,interpolated,0.003643,4.311,0.9942,0,275.2 +Y154d182,A/Utah/27/2022,plate2-TCCTTGTAATTCAACT,0.004559,interpolated,0.004559,16.05,1,0,219.3 +Y154d182,A/Washington/23/2020,plate2-ACGGAATCCCCTGAGA,0.001692,interpolated,0.001692,15,1,0,591 +Y154d182,A/Washington/23/2020,plate2-GAACTGGCGTCAATCA,0.001611,interpolated,0.001611,15.68,1,0,620.8 +Y154d182,A/Washington/23/2020,plate2-GGATAAGAAAACTACT,0.001536,interpolated,0.001536,13.24,1,0,650.8 +Y154d182,A/Wisconsin/588/2019,plate2-AGTCCTATCCTCAAAT,0.0006159,interpolated,0.0006323,2.26,0.9712,0,1624 +Y154d182,A/Wisconsin/588/2019,plate2-GAAGAAACTATAACCA,0.0008673,interpolated,0.0008721,3.401,0.9908,0,1153 +Y154d182,A/Wisconsin/588/2019,plate2-TATATTAGTAACATAA,0.001663,interpolated,0.001664,18.62,0.9961,0,601.2 diff --git a/test_example/results/sera/M099d0/titers_median.csv b/test_example/results/sera/M099d0/titers_median.csv new file mode 100644 index 0000000..b9fd3b9 --- /dev/null +++ b/test_example/results/sera/M099d0/titers_median.csv @@ -0,0 +1,37 @@ +serum,virus,nt50,n_replicates,nt50_stderr,nt50_bound +M099d0,A/Bangladesh/2221/2021,221.1,6,73.84,interpolated +M099d0,A/Bangladesh/3210810034/2021,196.9,4,97.86,interpolated +M099d0,A/Bangladesh/8002/2021,292.2,6,117.8,interpolated +M099d0,A/Bangladesh/8036/2021,285.3,6,63.76,interpolated +M099d0,A/Belgium/H0017/2022,566.1,6,38.77,interpolated +M099d0,A/Belgium/H0038/2022,820.1,6,202.5,interpolated +M099d0,A/Brisbane/02/2018,703.4,8,254.8,interpolated +M099d0,A/Brisbane/48/2022,210.8,6,63.33,interpolated +M099d0,A/California/07/2009,649.2,8,76.09,interpolated +M099d0,A/Chester/5355/2022,386.8,6,84.54,interpolated +M099d0,A/Cote_DIvoire/1448/2021,608.5,6,137.6,interpolated +M099d0,A/England/220200318/2022,632.2,6,189.4,interpolated +M099d0,A/Ghana/138/2020,702.2,6,83.55,interpolated 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+M099d0,A/Togo/0304/2021,723.4,6,122.7,interpolated +M099d0,A/Togo/845/2020,754.3,6,178.9,interpolated +M099d0,A/Utah/27/2022,216.2,6,43.03,interpolated +M099d0,A/Washington/23/2020,420,6,74.41,interpolated +M099d0,A/Wisconsin/588/2019,271.3,5,70.86,interpolated diff --git a/test_example/results/sera/M099d0/titers_per_replicate.csv b/test_example/results/sera/M099d0/titers_per_replicate.csv new file mode 100644 index 0000000..8478257 --- /dev/null +++ b/test_example/results/sera/M099d0/titers_per_replicate.csv @@ -0,0 +1,219 @@ +serum,replicate,virus,nt50,nt50_bound +M099d0,plate11-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,558.8,interpolated +M099d0,plate11-GACAGCAATGCATACA,A/Bangladesh/2221/2021,231.4,interpolated +M099d0,plate11-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,538.8,interpolated +M099d0,plate11-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,584.3,interpolated +M099d0,plate11-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,185.3,interpolated +M099d0,plate11-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,562.5,interpolated +M099d0,plate11-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,387.1,interpolated +M099d0,plate11-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,909.5,interpolated +M099d0,plate11-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,556.4,interpolated +M099d0,plate11-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,329.6,interpolated +M099d0,plate11-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,506.2,interpolated +M099d0,plate11-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,656.9,interpolated +M099d0,plate11-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,578.4,interpolated +M099d0,plate11-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,582,interpolated +M099d0,plate11-GATCCGTACTTTGATT,A/Belgium/H0038/2022,1433,interpolated +M099d0,plate11-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,490.2,interpolated +M099d0,plate11-TACCGTATAATTAAAA,A/Belgium/H0038/2022,1621,interpolated +M099d0,plate11-ACGACATGATCAAACG,A/Brisbane/02/2018,2642,interpolated 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+M099d0,plate11-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,623.6,interpolated +M099d0,plate11-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,617,interpolated +M099d0,plate11-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,1338,interpolated +M099d0,plate11-CGTAATACATTTAAGA,A/England/220200318/2022,1047,interpolated +M099d0,plate11-GACCAACTGTGGTACA,A/England/220200318/2022,1737,interpolated +M099d0,plate11-GCTGCGCCTAACATAA,A/England/220200318/2022,633.2,interpolated +M099d0,plate11-CCAGTTCCCTTCGATG,A/Ghana/138/2020,594.6,interpolated +M099d0,plate11-GACTATGGTCTAAAAA,A/Ghana/138/2020,1065,interpolated +M099d0,plate11-TAAGCCATAAATCAAT,A/Ghana/138/2020,973.4,interpolated +M099d0,plate11-CAGCAAAAGCATCACC,A/Ghana/2080/2020,599.6,interpolated +M099d0,plate11-GCAATCCCGCAATTTG,A/Ghana/2080/2020,712.3,interpolated +M099d0,plate11-GTAGTGCATCATTGAT,A/Ghana/2080/2020,622.7,interpolated +M099d0,plate11-ACATGAATTCAGACGG,A/Hawaii/70/2019,1143,interpolated +M099d0,plate11-AGTAAACATGCATTGG,A/Hawaii/70/2019,662.1,interpolated +M099d0,plate11-ATAGAATCGCAAATTA,A/Hawaii/70/2019,610.9,interpolated +M099d0,plate11-TGGAATCGTCACCGAT,A/Hawaii/70/2019,1536,interpolated +M099d0,plate11-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,575.6,interpolated +M099d0,plate11-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,553.8,interpolated +M099d0,plate11-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,470.1,interpolated +M099d0,plate11-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,209.6,interpolated +M099d0,plate11-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,275.1,interpolated +M099d0,plate11-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,363.8,interpolated +M099d0,plate11-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,433.1,interpolated +M099d0,plate11-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,533.6,interpolated +M099d0,plate11-AACGTTAACAAATGAA,A/Michigan/19/2021,956.9,interpolated +M099d0,plate11-AGAGAAAAAACAGTGA,A/Michigan/19/2021,676.4,interpolated +M099d0,plate11-TAATGAGCTTTATGGT,A/Michigan/19/2021,557.9,interpolated +M099d0,plate11-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,1610,interpolated +M099d0,plate11-CACCTAGGATCGCACT,A/Michigan/45/2015,1112,interpolated +M099d0,plate11-TGAGGATAATCACAAG,A/Michigan/45/2015,967,interpolated +M099d0,plate11-TTGAAAAAATCATAAA,A/Michigan/45/2015,1484,interpolated +M099d0,plate11-CAAATATATCTTCATG,A/Newcastle/2/2022,426.7,interpolated +M099d0,plate11-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,392.9,interpolated +M099d0,plate11-TTCACTAAGATTTCAT,A/Newcastle/2/2022,559,interpolated +M099d0,plate11-AAATAAGTACGCAAAT,A/Niger/10217/2021,972.1,interpolated +M099d0,plate11-CATCAACCGCCATTTC,A/Niger/10217/2021,583.4,interpolated +M099d0,plate11-GAACGATTGTAATTTT,A/Niger/10217/2021,755.4,interpolated +M099d0,plate11-ACCTTACTAAATCCTG,A/Nimes/871/2021,1670,interpolated +M099d0,plate11-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,1210,interpolated +M099d0,plate11-TAATTACATTGCGGTT,A/Nimes/871/2021,1679,interpolated +M099d0,plate11-GACTCAATAATCACAC,A/Norway/25089/2022,273.4,interpolated +M099d0,plate11-TGGAAAAGATGTAATA,A/Norway/25089/2022,559.2,interpolated +M099d0,plate11-ACATAAGAACCCTATA,A/Paris/30353/2021,582.7,interpolated +M099d0,plate11-ACATTTCCCTCGATAT,A/Paris/30353/2021,827.1,interpolated +M099d0,plate11-GTTTGACAATCACTAC,A/Paris/30353/2021,1155,interpolated +M099d0,plate11-AAACTAAAAGCAAGGG,A/Paris/31196/2021,1029,interpolated +M099d0,plate11-AATAAGTATACGGGAT,A/Paris/31196/2021,1151,interpolated +M099d0,plate11-AGCAGCCTGAAAATAT,A/Paris/31196/2021,1684,interpolated +M099d0,plate11-AGCCCCGTGAGAAGCA,A/Perth/1/2022,555,interpolated +M099d0,plate11-CTGCACGAGAGACTTC,A/Perth/1/2022,511.1,interpolated +M099d0,plate11-TTGGGGAAATATATAA,A/Perth/1/2022,544.9,interpolated +M099d0,plate11-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,580.6,interpolated +M099d0,plate11-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,551.7,interpolated +M099d0,plate11-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,565,interpolated +M099d0,plate11-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,658,interpolated +M099d0,plate11-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,649.5,interpolated +M099d0,plate11-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,1214,interpolated +M099d0,plate11-CTATTAATCATGCAAA,A/Sydney/43/2022,442.7,interpolated +M099d0,plate11-TACGGACATTCTTAAC,A/Sydney/43/2022,296.3,interpolated +M099d0,plate11-TAGTATAATAGAGCAG,A/Sydney/43/2022,206.2,interpolated +M099d0,plate11-AACGAATGAATTTCTT,A/Togo/0274/2021,959,interpolated +M099d0,plate11-GTAACATTATACGATT,A/Togo/0274/2021,989.5,interpolated +M099d0,plate11-TAGCAGATGTATCAAT,A/Togo/0274/2021,1177,interpolated +M099d0,plate11-AACTCTAAAGATATAA,A/Togo/0304/2021,614.2,interpolated +M099d0,plate11-AGAGATAATAACAAAA,A/Togo/0304/2021,637,interpolated +M099d0,plate11-GAAGAATGGTTTTCTG,A/Togo/0304/2021,1313,interpolated +M099d0,plate11-AGGTCAAGACCACAGG,A/Togo/845/2020,836,interpolated +M099d0,plate11-GCATGGATCCTTTACT,A/Togo/845/2020,1642,interpolated +M099d0,plate11-TTACCGTCTACGCATA,A/Togo/845/2020,1385,interpolated +M099d0,plate11-ACAATGTGACTCACCC,A/Utah/27/2022,464.7,interpolated +M099d0,plate11-TAAATAACTCGTATTT,A/Utah/27/2022,232.5,interpolated +M099d0,plate11-TCCTTGTAATTCAACT,A/Utah/27/2022,298.9,interpolated +M099d0,plate11-ACGGAATCCCCTGAGA,A/Washington/23/2020,511.3,interpolated +M099d0,plate11-GAACTGGCGTCAATCA,A/Washington/23/2020,640.7,interpolated +M099d0,plate11-GGATAAGAAAACTACT,A/Washington/23/2020,543.6,interpolated +M099d0,plate11-GAAGAAACTATAACCA,A/Wisconsin/588/2019,379.3,interpolated +M099d0,plate11-TATATTAGTAACATAA,A/Wisconsin/588/2019,568.5,interpolated +M099d0,plate2-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,210.8,interpolated +M099d0,plate2-GACAGCAATGCATACA,A/Bangladesh/2221/2021,163.2,interpolated +M099d0,plate2-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,200.1,interpolated +M099d0,plate2-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,200.5,interpolated +M099d0,plate2-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,193.4,interpolated +M099d0,plate2-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,197.3,interpolated +M099d0,plate2-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,182.7,interpolated +M099d0,plate2-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,195.6,interpolated +M099d0,plate2-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,204.9,interpolated +M099d0,plate2-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,200.9,interpolated +M099d0,plate2-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,241,interpolated +M099d0,plate2-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,553.9,interpolated +M099d0,plate2-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,401.2,interpolated +M099d0,plate2-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,446.2,interpolated +M099d0,plate2-GATCCGTACTTTGATT,A/Belgium/H0038/2022,623.2,interpolated +M099d0,plate2-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,1017,interpolated +M099d0,plate2-TACCGTATAATTAAAA,A/Belgium/H0038/2022,476.6,interpolated +M099d0,plate2-ACGACATGATCAAACG,A/Brisbane/02/2018,1502,interpolated +M099d0,plate2-ATCCGATTTAAAGGCA,A/Brisbane/02/2018,660.2,interpolated +M099d0,plate2-TAATAAGCCAGCAAGA,A/Brisbane/02/2018,562.3,interpolated +M099d0,plate2-TTGGGCACTAAATTAA,A/Brisbane/02/2018,631.5,interpolated +M099d0,plate2-CCCTATGCTGCGTATT,A/Brisbane/48/2022,201.7,interpolated +M099d0,plate2-GAGCTCTAAAGCAACA,A/Brisbane/48/2022,212,interpolated +M099d0,plate2-TTATGATCTAAACAGA,A/Brisbane/48/2022,201.2,interpolated +M099d0,plate2-CATGTGAATTCGCCCA,A/California/07/2009,610.2,interpolated +M099d0,plate2-CCTTTCTCAAAACATA,A/California/07/2009,1088,interpolated +M099d0,plate2-CGCCTAATGTTAATAA,A/California/07/2009,1090,interpolated +M099d0,plate2-GACACAGAACCCATGC,A/California/07/2009,676.1,interpolated +M099d0,plate2-AAAAAACGCATGTAGA,A/Chester/5355/2022,190.3,interpolated +M099d0,plate2-CCTCAAAATAACAAGC,A/Chester/5355/2022,205.3,interpolated +M099d0,plate2-TCATATAAAGAAAAGG,A/Chester/5355/2022,197.3,interpolated +M099d0,plate2-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,599.9,interpolated +M099d0,plate2-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,342.3,interpolated +M099d0,plate2-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,592.2,interpolated +M099d0,plate2-CGTAATACATTTAAGA,A/England/220200318/2022,631.1,interpolated +M099d0,plate2-GACCAACTGTGGTACA,A/England/220200318/2022,566.2,interpolated +M099d0,plate2-GCTGCGCCTAACATAA,A/England/220200318/2022,572.9,interpolated +M099d0,plate2-CCAGTTCCCTTCGATG,A/Ghana/138/2020,606.3,interpolated +M099d0,plate2-GACTATGGTCTAAAAA,A/Ghana/138/2020,787,interpolated +M099d0,plate2-TAAGCCATAAATCAAT,A/Ghana/138/2020,617.5,interpolated +M099d0,plate2-CAGCAAAAGCATCACC,A/Ghana/2080/2020,528.5,interpolated +M099d0,plate2-GCAATCCCGCAATTTG,A/Ghana/2080/2020,895.3,interpolated +M099d0,plate2-GTAGTGCATCATTGAT,A/Ghana/2080/2020,653,interpolated +M099d0,plate2-ACATGAATTCAGACGG,A/Hawaii/70/2019,591.3,interpolated +M099d0,plate2-AGTAAACATGCATTGG,A/Hawaii/70/2019,520.7,interpolated +M099d0,plate2-ATAGAATCGCAAATTA,A/Hawaii/70/2019,559.6,interpolated +M099d0,plate2-TGGAATCGTCACCGAT,A/Hawaii/70/2019,698,interpolated +M099d0,plate2-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,203.5,interpolated +M099d0,plate2-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,198.3,interpolated +M099d0,plate2-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,252.5,interpolated +M099d0,plate2-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,178.1,interpolated +M099d0,plate2-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,174.8,interpolated +M099d0,plate2-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,195.8,interpolated +M099d0,plate2-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,213,interpolated +M099d0,plate2-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,192.9,interpolated +M099d0,plate2-AACGTTAACAAATGAA,A/Michigan/19/2021,199,interpolated +M099d0,plate2-AGAGAAAAAACAGTGA,A/Michigan/19/2021,189.3,interpolated +M099d0,plate2-TAATGAGCTTTATGGT,A/Michigan/19/2021,207.8,interpolated +M099d0,plate2-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,565.2,interpolated +M099d0,plate2-CACCTAGGATCGCACT,A/Michigan/45/2015,866.4,interpolated +M099d0,plate2-TGAGGATAATCACAAG,A/Michigan/45/2015,1029,interpolated +M099d0,plate2-TTGAAAAAATCATAAA,A/Michigan/45/2015,666.1,interpolated +M099d0,plate2-CAAATATATCTTCATG,A/Newcastle/2/2022,200.6,interpolated +M099d0,plate2-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,231.7,interpolated +M099d0,plate2-TTCACTAAGATTTCAT,A/Newcastle/2/2022,192.4,interpolated +M099d0,plate2-AAATAAGTACGCAAAT,A/Niger/10217/2021,507.8,interpolated +M099d0,plate2-CATCAACCGCCATTTC,A/Niger/10217/2021,1027,interpolated +M099d0,plate2-GAACGATTGTAATTTT,A/Niger/10217/2021,653.2,interpolated +M099d0,plate2-ACCTTACTAAATCCTG,A/Nimes/871/2021,840.2,interpolated +M099d0,plate2-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,643.4,interpolated +M099d0,plate2-TAATTACATTGCGGTT,A/Nimes/871/2021,391.9,interpolated +M099d0,plate2-CGGATAAAAATGATAT,A/Norway/25089/2022,214.8,interpolated +M099d0,plate2-GACTCAATAATCACAC,A/Norway/25089/2022,174,interpolated +M099d0,plate2-TGGAAAAGATGTAATA,A/Norway/25089/2022,183.8,interpolated +M099d0,plate2-ACATAAGAACCCTATA,A/Paris/30353/2021,567.7,interpolated +M099d0,plate2-ACATTTCCCTCGATAT,A/Paris/30353/2021,585.4,interpolated +M099d0,plate2-GTTTGACAATCACTAC,A/Paris/30353/2021,769.6,interpolated +M099d0,plate2-AAACTAAAAGCAAGGG,A/Paris/31196/2021,900.7,interpolated +M099d0,plate2-AATAAGTATACGGGAT,A/Paris/31196/2021,937.6,interpolated +M099d0,plate2-AGCAGCCTGAAAATAT,A/Paris/31196/2021,691.6,interpolated +M099d0,plate2-AGCCCCGTGAGAAGCA,A/Perth/1/2022,202.1,interpolated +M099d0,plate2-CTGCACGAGAGACTTC,A/Perth/1/2022,192,interpolated +M099d0,plate2-TTGGGGAAATATATAA,A/Perth/1/2022,204.5,interpolated +M099d0,plate2-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,294.7,interpolated +M099d0,plate2-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,256.3,interpolated +M099d0,plate2-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,243,interpolated +M099d0,plate2-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,1341,interpolated +M099d0,plate2-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,871.1,interpolated +M099d0,plate2-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,258,interpolated +M099d0,plate2-CTATTAATCATGCAAA,A/Sydney/43/2022,202.2,interpolated +M099d0,plate2-TACGGACATTCTTAAC,A/Sydney/43/2022,195.2,interpolated +M099d0,plate2-TAGTATAATAGAGCAG,A/Sydney/43/2022,289,interpolated +M099d0,plate2-AACGAATGAATTTCTT,A/Togo/0274/2021,557.1,interpolated +M099d0,plate2-GTAACATTATACGATT,A/Togo/0274/2021,704.2,interpolated +M099d0,plate2-TAGCAGATGTATCAAT,A/Togo/0274/2021,341.9,interpolated +M099d0,plate2-AACTCTAAAGATATAA,A/Togo/0304/2021,809.8,interpolated +M099d0,plate2-AGAGATAATAACAAAA,A/Togo/0304/2021,1086,interpolated +M099d0,plate2-GAAGAATGGTTTTCTG,A/Togo/0304/2021,567.2,interpolated +M099d0,plate2-AGGTCAAGACCACAGG,A/Togo/845/2020,667,interpolated +M099d0,plate2-GCATGGATCCTTTACT,A/Togo/845/2020,598.1,interpolated 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+M099d30,A/Bangladesh/2221/2021,1534,6,187.6,interpolated +M099d30,A/Bangladesh/3210810034/2021,1456,4,112.7,interpolated +M099d30,A/Bangladesh/8002/2021,1646,6,230.4,interpolated +M099d30,A/Bangladesh/8036/2021,1678,6,43.41,interpolated +M099d30,A/Belgium/H0017/2022,2516,6,501.1,interpolated +M099d30,A/Belgium/H0038/2022,2532,6,613.8,interpolated +M099d30,A/Brisbane/02/2018,5376,8,1014,interpolated +M099d30,A/Brisbane/48/2022,1397,6,57.84,interpolated +M099d30,A/California/07/2009,4680,8,938.3,interpolated +M099d30,A/Chester/5355/2022,1419,6,682.8,interpolated +M099d30,A/Cote_DIvoire/1448/2021,3237,6,412.6,interpolated +M099d30,A/England/220200318/2022,2696,6,561,interpolated +M099d30,A/Ghana/138/2020,1824,6,426.4,interpolated +M099d30,A/Ghana/2080/2020,2974,6,496.5,interpolated +M099d30,A/Hawaii/70/2019,3124,8,421.3,interpolated +M099d30,A/India-PUN-NIV328484/2021,1970,6,602.3,interpolated +M099d30,A/India-Pune-Nivcov2221170/2022,1015,4,21.79,interpolated +M099d30,A/India/Pun-NIV312851/2021,1658,6,599.8,interpolated +M099d30,A/Michigan/19/2021,1720,6,26.97,interpolated +M099d30,A/Michigan/45/2015,5283,8,1399,interpolated +M099d30,A/Newcastle/2/2022,1550,6,336.4,interpolated +M099d30,A/Niger/10217/2021,1738,6,124.7,interpolated +M099d30,A/Nimes/871/2021,3310,6,392.1,interpolated +M099d30,A/Norway/25089/2022,646,6,160,interpolated +M099d30,A/Paris/30353/2021,1696,6,358.6,interpolated +M099d30,A/Paris/31196/2021,3300,6,1342,interpolated +M099d30,A/Perth/1/2022,1760,6,147.2,interpolated +M099d30,A/SouthAfrica/R14850/2021,1088,6,145,interpolated +M099d30,A/SouthAfrica/R16462/2021,1868,6,425.8,interpolated +M099d30,A/Sydney/43/2022,1187,6,346.5,interpolated +M099d30,A/Togo/0274/2021,2726,6,315.8,interpolated +M099d30,A/Togo/0304/2021,1828,6,494.7,interpolated +M099d30,A/Togo/845/2020,1972,6,169.5,interpolated +M099d30,A/Utah/27/2022,1410,6,119.8,interpolated +M099d30,A/Washington/23/2020,2549,6,433.3,interpolated +M099d30,A/Wisconsin/588/2019,2348,6,534.9,interpolated diff --git a/test_example/results/sera/M099d30/titers_per_replicate.csv b/test_example/results/sera/M099d30/titers_per_replicate.csv new file mode 100644 index 0000000..c49c506 --- /dev/null +++ b/test_example/results/sera/M099d30/titers_per_replicate.csv @@ -0,0 +1,221 @@ +serum,replicate,virus,nt50,nt50_bound +M099d30,plate11-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,647.2,interpolated +M099d30,plate11-GACAGCAATGCATACA,A/Bangladesh/2221/2021,1827,interpolated +M099d30,plate11-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,1760,interpolated +M099d30,plate11-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,1077,interpolated +M099d30,plate11-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,1539,interpolated +M099d30,plate11-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,1586,interpolated +M099d30,plate11-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,648.2,interpolated +M099d30,plate11-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,1716,interpolated +M099d30,plate11-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,1682,interpolated +M099d30,plate11-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,1420,interpolated +M099d30,plate11-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,1681,interpolated +M099d30,plate11-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,1808,interpolated +M099d30,plate11-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,1625,interpolated +M099d30,plate11-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,1878,interpolated +M099d30,plate11-GATCCGTACTTTGATT,A/Belgium/H0038/2022,1471,interpolated +M099d30,plate11-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,1692,interpolated +M099d30,plate11-TACCGTATAATTAAAA,A/Belgium/H0038/2022,1874,interpolated +M099d30,plate11-ACGACATGATCAAACG,A/Brisbane/02/2018,5248,interpolated +M099d30,plate11-ATCCGATTTAAAGGCA,A/Brisbane/02/2018,1816,interpolated +M099d30,plate11-TAATAAGCCAGCAAGA,A/Brisbane/02/2018,6334,interpolated +M099d30,plate11-TTGGGCACTAAATTAA,A/Brisbane/02/2018,3611,interpolated +M099d30,plate11-CCCTATGCTGCGTATT,A/Brisbane/48/2022,1556,interpolated +M099d30,plate11-GAGCTCTAAAGCAACA,A/Brisbane/48/2022,1373,interpolated +M099d30,plate11-TTATGATCTAAACAGA,A/Brisbane/48/2022,1418,interpolated +M099d30,plate11-CATGTGAATTCGCCCA,A/California/07/2009,7489,interpolated +M099d30,plate11-CCTTTCTCAAAACATA,A/California/07/2009,3216,interpolated +M099d30,plate11-CGCCTAATGTTAATAA,A/California/07/2009,1825,interpolated +M099d30,plate11-GACACAGAACCCATGC,A/California/07/2009,3543,interpolated +M099d30,plate11-AAAAAACGCATGTAGA,A/Chester/5355/2022,1043,interpolated +M099d30,plate11-CCTCAAAATAACAAGC,A/Chester/5355/2022,5450,interpolated +M099d30,plate11-TCATATAAAGAAAAGG,A/Chester/5355/2022,1673,interpolated +M099d30,plate11-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,2931,interpolated +M099d30,plate11-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,1969,interpolated +M099d30,plate11-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,1870,interpolated +M099d30,plate11-CGTAATACATTTAAGA,A/England/220200318/2022,1969,interpolated +M099d30,plate11-GACCAACTGTGGTACA,A/England/220200318/2022,1905,interpolated +M099d30,plate11-GCTGCGCCTAACATAA,A/England/220200318/2022,1651,interpolated +M099d30,plate11-CCAGTTCCCTTCGATG,A/Ghana/138/2020,1713,interpolated +M099d30,plate11-GACTATGGTCTAAAAA,A/Ghana/138/2020,1712,interpolated +M099d30,plate11-TAAGCCATAAATCAAT,A/Ghana/138/2020,1735,interpolated +M099d30,plate11-CAGCAAAAGCATCACC,A/Ghana/2080/2020,2895,interpolated +M099d30,plate11-GCAATCCCGCAATTTG,A/Ghana/2080/2020,2835,interpolated +M099d30,plate11-GTAGTGCATCATTGAT,A/Ghana/2080/2020,3053,interpolated +M099d30,plate11-ACATGAATTCAGACGG,A/Hawaii/70/2019,1809,interpolated +M099d30,plate11-AGTAAACATGCATTGG,A/Hawaii/70/2019,2249,interpolated +M099d30,plate11-ATAGAATCGCAAATTA,A/Hawaii/70/2019,2678,interpolated +M099d30,plate11-TGGAATCGTCACCGAT,A/Hawaii/70/2019,4635,interpolated +M099d30,plate11-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,5376,interpolated +M099d30,plate11-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,1639,interpolated +M099d30,plate11-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,1816,interpolated +M099d30,plate11-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,1058,interpolated +M099d30,plate11-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,956.9,interpolated +M099d30,plate11-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,4743,interpolated +M099d30,plate11-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,1496,interpolated +M099d30,plate11-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,1252,interpolated +M099d30,plate11-AACGTTAACAAATGAA,A/Michigan/19/2021,1720,interpolated +M099d30,plate11-AGAGAAAAAACAGTGA,A/Michigan/19/2021,1692,interpolated +M099d30,plate11-TAATGAGCTTTATGGT,A/Michigan/19/2021,1875,interpolated +M099d30,plate11-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,4872,interpolated +M099d30,plate11-CACCTAGGATCGCACT,A/Michigan/45/2015,5526,interpolated +M099d30,plate11-TGAGGATAATCACAAG,A/Michigan/45/2015,5134,interpolated +M099d30,plate11-TTGAAAAAATCATAAA,A/Michigan/45/2015,1.624e+04,interpolated +M099d30,plate11-CAAATATATCTTCATG,A/Newcastle/2/2022,2796,interpolated +M099d30,plate11-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,1318,interpolated +M099d30,plate11-TTCACTAAGATTTCAT,A/Newcastle/2/2022,674.1,interpolated +M099d30,plate11-AAATAAGTACGCAAAT,A/Niger/10217/2021,1724,interpolated +M099d30,plate11-CATCAACCGCCATTTC,A/Niger/10217/2021,1501,interpolated +M099d30,plate11-GAACGATTGTAATTTT,A/Niger/10217/2021,1681,interpolated +M099d30,plate11-ACCTTACTAAATCCTG,A/Nimes/871/2021,3137,interpolated +M099d30,plate11-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,2653,interpolated +M099d30,plate11-TAATTACATTGCGGTT,A/Nimes/871/2021,4189,interpolated +M099d30,plate11-CGGATAAAAATGATAT,A/Norway/25089/2022,257.4,interpolated +M099d30,plate11-GACTCAATAATCACAC,A/Norway/25089/2022,717.1,interpolated +M099d30,plate11-TGGAAAAGATGTAATA,A/Norway/25089/2022,253.1,interpolated +M099d30,plate11-ACATAAGAACCCTATA,A/Paris/30353/2021,1685,interpolated +M099d30,plate11-ACATTTCCCTCGATAT,A/Paris/30353/2021,1253,interpolated +M099d30,plate11-GTTTGACAATCACTAC,A/Paris/30353/2021,1707,interpolated +M099d30,plate11-AAACTAAAAGCAAGGG,A/Paris/31196/2021,1442,interpolated +M099d30,plate11-AATAAGTATACGGGAT,A/Paris/31196/2021,1.035e+04,interpolated +M099d30,plate11-AGCAGCCTGAAAATAT,A/Paris/31196/2021,1774,interpolated +M099d30,plate11-AGCCCCGTGAGAAGCA,A/Perth/1/2022,1710,interpolated +M099d30,plate11-CTGCACGAGAGACTTC,A/Perth/1/2022,1686,interpolated +M099d30,plate11-TTGGGGAAATATATAA,A/Perth/1/2022,1570,interpolated +M099d30,plate11-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,994.9,interpolated +M099d30,plate11-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,626.1,interpolated +M099d30,plate11-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,612.9,interpolated +M099d30,plate11-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,1704,interpolated +M099d30,plate11-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,1746,interpolated +M099d30,plate11-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,1837,interpolated +M099d30,plate11-CTATTAATCATGCAAA,A/Sydney/43/2022,645.1,interpolated +M099d30,plate11-TACGGACATTCTTAAC,A/Sydney/43/2022,1197,interpolated +M099d30,plate11-TAGTATAATAGAGCAG,A/Sydney/43/2022,1177,interpolated +M099d30,plate11-AACGAATGAATTTCTT,A/Togo/0274/2021,1813,interpolated +M099d30,plate11-GTAACATTATACGATT,A/Togo/0274/2021,1850,interpolated +M099d30,plate11-TAGCAGATGTATCAAT,A/Togo/0274/2021,2669,interpolated +M099d30,plate11-AACTCTAAAGATATAA,A/Togo/0304/2021,1850,interpolated +M099d30,plate11-AGAGATAATAACAAAA,A/Togo/0304/2021,1732,interpolated +M099d30,plate11-GAAGAATGGTTTTCTG,A/Togo/0304/2021,1805,interpolated +M099d30,plate11-AGGTCAAGACCACAGG,A/Togo/845/2020,1709,interpolated +M099d30,plate11-GCATGGATCCTTTACT,A/Togo/845/2020,1662,interpolated +M099d30,plate11-TTACCGTCTACGCATA,A/Togo/845/2020,1740,interpolated +M099d30,plate11-ACAATGTGACTCACCC,A/Utah/27/2022,1302,interpolated +M099d30,plate11-TAAATAACTCGTATTT,A/Utah/27/2022,1231,interpolated +M099d30,plate11-TCCTTGTAATTCAACT,A/Utah/27/2022,1277,interpolated +M099d30,plate11-ACGGAATCCCCTGAGA,A/Washington/23/2020,935.6,interpolated +M099d30,plate11-GAACTGGCGTCAATCA,A/Washington/23/2020,2026,interpolated +M099d30,plate11-GGATAAGAAAACTACT,A/Washington/23/2020,1794,interpolated +M099d30,plate11-AGTCCTATCCTCAAAT,A/Wisconsin/588/2019,2834,interpolated +M099d30,plate11-GAAGAAACTATAACCA,A/Wisconsin/588/2019,1666,interpolated +M099d30,plate11-TATATTAGTAACATAA,A/Wisconsin/588/2019,1862,interpolated +M099d30,plate2-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,1671,interpolated +M099d30,plate2-GACAGCAATGCATACA,A/Bangladesh/2221/2021,1396,interpolated +M099d30,plate2-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,1077,interpolated +M099d30,plate2-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,1569,interpolated +M099d30,plate2-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,1374,interpolated +M099d30,plate2-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,674,interpolated +M099d30,plate2-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,1925,interpolated +M099d30,plate2-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,1705,interpolated +M099d30,plate2-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,1701,interpolated +M099d30,plate2-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,1676,interpolated +M099d30,plate2-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,1633,interpolated +M099d30,plate2-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,3864,interpolated +M099d30,plate2-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,4550,interpolated +M099d30,plate2-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,3155,interpolated +M099d30,plate2-GATCCGTACTTTGATT,A/Belgium/H0038/2022,3190,interpolated +M099d30,plate2-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,5260,interpolated +M099d30,plate2-TACCGTATAATTAAAA,A/Belgium/H0038/2022,3946,interpolated +M099d30,plate2-ACGACATGATCAAACG,A/Brisbane/02/2018,1.164e+04,interpolated +M099d30,plate2-ATCCGATTTAAAGGCA,A/Brisbane/02/2018,5710,interpolated +M099d30,plate2-TAATAAGCCAGCAAGA,A/Brisbane/02/2018,5505,interpolated +M099d30,plate2-TTGGGCACTAAATTAA,A/Brisbane/02/2018,4127,interpolated +M099d30,plate2-CCCTATGCTGCGTATT,A/Brisbane/48/2022,1320,interpolated +M099d30,plate2-GAGCTCTAAAGCAACA,A/Brisbane/48/2022,1376,interpolated +M099d30,plate2-TTATGATCTAAACAGA,A/Brisbane/48/2022,1695,interpolated +M099d30,plate2-CATGTGAATTCGCCCA,A/California/07/2009,5349,interpolated +M099d30,plate2-CCTTTCTCAAAACATA,A/California/07/2009,1.024e+04,interpolated +M099d30,plate2-CGCCTAATGTTAATAA,A/California/07/2009,4497,interpolated +M099d30,plate2-GACACAGAACCCATGC,A/California/07/2009,4863,interpolated +M099d30,plate2-AAAAAACGCATGTAGA,A/Chester/5355/2022,1361,interpolated +M099d30,plate2-CCTCAAAATAACAAGC,A/Chester/5355/2022,1427,interpolated +M099d30,plate2-TCATATAAAGAAAAGG,A/Chester/5355/2022,1411,interpolated +M099d30,plate2-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,4466,interpolated +M099d30,plate2-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,3543,interpolated +M099d30,plate2-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,3583,interpolated +M099d30,plate2-CGTAATACATTTAAGA,A/England/220200318/2022,4247,interpolated +M099d30,plate2-GACCAACTGTGGTACA,A/England/220200318/2022,3424,interpolated +M099d30,plate2-GCTGCGCCTAACATAA,A/England/220200318/2022,4904,interpolated +M099d30,plate2-CCAGTTCCCTTCGATG,A/Ghana/138/2020,1944,interpolated +M099d30,plate2-GACTATGGTCTAAAAA,A/Ghana/138/2020,1912,interpolated +M099d30,plate2-TAAGCCATAAATCAAT,A/Ghana/138/2020,4349,interpolated +M099d30,plate2-CAGCAAAAGCATCACC,A/Ghana/2080/2020,2722,interpolated +M099d30,plate2-GCAATCCCGCAATTTG,A/Ghana/2080/2020,5444,interpolated +M099d30,plate2-GTAGTGCATCATTGAT,A/Ghana/2080/2020,4963,interpolated +M099d30,plate2-ACATGAATTCAGACGG,A/Hawaii/70/2019,2941,interpolated +M099d30,plate2-AGTAAACATGCATTGG,A/Hawaii/70/2019,3306,interpolated +M099d30,plate2-ATAGAATCGCAAATTA,A/Hawaii/70/2019,4872,interpolated +M099d30,plate2-TGGAATCGTCACCGAT,A/Hawaii/70/2019,4685,interpolated +M099d30,plate2-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,1547,interpolated +M099d30,plate2-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,3152,interpolated +M099d30,plate2-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,2124,interpolated +M099d30,plate2-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,998.2,interpolated +M099d30,plate2-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,1031,interpolated +M099d30,plate2-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,2680,interpolated +M099d30,plate2-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,1819,interpolated +M099d30,plate2-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,580.2,interpolated +M099d30,plate2-AACGTTAACAAATGAA,A/Michigan/19/2021,1718,interpolated +M099d30,plate2-AGAGAAAAAACAGTGA,A/Michigan/19/2021,1758,interpolated +M099d30,plate2-TAATGAGCTTTATGGT,A/Michigan/19/2021,1720,interpolated +M099d30,plate2-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,4503,interpolated +M099d30,plate2-CACCTAGGATCGCACT,A/Michigan/45/2015,4953,interpolated +M099d30,plate2-TGAGGATAATCACAAG,A/Michigan/45/2015,8125,interpolated +M099d30,plate2-TTGAAAAAATCATAAA,A/Michigan/45/2015,5432,interpolated +M099d30,plate2-CAAATATATCTTCATG,A/Newcastle/2/2022,2159,interpolated +M099d30,plate2-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,772.9,interpolated +M099d30,plate2-TTCACTAAGATTTCAT,A/Newcastle/2/2022,1781,interpolated +M099d30,plate2-AAATAAGTACGCAAAT,A/Niger/10217/2021,2395,interpolated +M099d30,plate2-CATCAACCGCCATTTC,A/Niger/10217/2021,1751,interpolated +M099d30,plate2-GAACGATTGTAATTTT,A/Niger/10217/2021,1847,interpolated +M099d30,plate2-ACCTTACTAAATCCTG,A/Nimes/871/2021,3483,interpolated +M099d30,plate2-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,1784,interpolated +M099d30,plate2-TAATTACATTGCGGTT,A/Nimes/871/2021,4326,interpolated +M099d30,plate2-CGGATAAAAATGATAT,A/Norway/25089/2022,675.9,interpolated +M099d30,plate2-GACTCAATAATCACAC,A/Norway/25089/2022,616.2,interpolated +M099d30,plate2-TGGAAAAGATGTAATA,A/Norway/25089/2022,1321,interpolated +M099d30,plate2-ACATAAGAACCCTATA,A/Paris/30353/2021,3082,interpolated +M099d30,plate2-ACATTTCCCTCGATAT,A/Paris/30353/2021,1636,interpolated +M099d30,plate2-GTTTGACAATCACTAC,A/Paris/30353/2021,3380,interpolated +M099d30,plate2-AAACTAAAAGCAAGGG,A/Paris/31196/2021,3361,interpolated +M099d30,plate2-AATAAGTATACGGGAT,A/Paris/31196/2021,5259,interpolated +M099d30,plate2-AGCAGCCTGAAAATAT,A/Paris/31196/2021,3239,interpolated +M099d30,plate2-AGCCCCGTGAGAAGCA,A/Perth/1/2022,1829,interpolated +M099d30,plate2-CTGCACGAGAGACTTC,A/Perth/1/2022,1809,interpolated +M099d30,plate2-TTGGGGAAATATATAA,A/Perth/1/2022,2574,interpolated +M099d30,plate2-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,1501,interpolated +M099d30,plate2-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,1182,interpolated +M099d30,plate2-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,1247,interpolated +M099d30,plate2-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,4071,interpolated +M099d30,plate2-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,3490,interpolated +M099d30,plate2-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,1899,interpolated +M099d30,plate2-CTATTAATCATGCAAA,A/Sydney/43/2022,1115,interpolated +M099d30,plate2-TACGGACATTCTTAAC,A/Sydney/43/2022,1584,interpolated +M099d30,plate2-TAGTATAATAGAGCAG,A/Sydney/43/2022,3089,interpolated +M099d30,plate2-AACGAATGAATTTCTT,A/Togo/0274/2021,3637,interpolated +M099d30,plate2-GTAACATTATACGATT,A/Togo/0274/2021,2783,interpolated +M099d30,plate2-TAGCAGATGTATCAAT,A/Togo/0274/2021,3473,interpolated +M099d30,plate2-AACTCTAAAGATATAA,A/Togo/0304/2021,1511,interpolated +M099d30,plate2-AGAGATAATAACAAAA,A/Togo/0304/2021,4146,interpolated +M099d30,plate2-GAAGAATGGTTTTCTG,A/Togo/0304/2021,3969,interpolated +M099d30,plate2-AGGTCAAGACCACAGG,A/Togo/845/2020,2203,interpolated +M099d30,plate2-GCATGGATCCTTTACT,A/Togo/845/2020,2547,interpolated +M099d30,plate2-TTACCGTCTACGCATA,A/Togo/845/2020,2530,interpolated +M099d30,plate2-ACAATGTGACTCACCC,A/Utah/27/2022,1519,interpolated +M099d30,plate2-TAAATAACTCGTATTT,A/Utah/27/2022,1597,interpolated +M099d30,plate2-TCCTTGTAATTCAACT,A/Utah/27/2022,2010,interpolated +M099d30,plate2-ACGGAATCCCCTGAGA,A/Washington/23/2020,3828,interpolated +M099d30,plate2-GAACTGGCGTCAATCA,A/Washington/23/2020,3117,interpolated +M099d30,plate2-GGATAAGAAAACTACT,A/Washington/23/2020,3072,interpolated +M099d30,plate2-AGTCCTATCCTCAAAT,A/Wisconsin/588/2019,1837,interpolated +M099d30,plate2-GAAGAAACTATAACCA,A/Wisconsin/588/2019,4352,interpolated +M099d30,plate2-TATATTAGTAACATAA,A/Wisconsin/588/2019,4560,interpolated diff --git a/test_example/results/sera/Y044d30/titers_median.csv b/test_example/results/sera/Y044d30/titers_median.csv new file mode 100644 index 0000000..c8423c5 --- /dev/null +++ b/test_example/results/sera/Y044d30/titers_median.csv @@ -0,0 +1,37 @@ +serum,virus,nt50,n_replicates,nt50_stderr,nt50_bound +Y044d30,A/Bangladesh/2221/2021,2125,3,881.8,interpolated +Y044d30,A/Bangladesh/3210810034/2021,535.2,2,67.55,interpolated +Y044d30,A/Bangladesh/8002/2021,1204,3,114.1,interpolated +Y044d30,A/Bangladesh/8036/2021,1641,3,1227,interpolated +Y044d30,A/Belgium/H0017/2022,1.443e+04,3,1161,interpolated +Y044d30,A/Belgium/H0038/2022,1.442e+04,3,497.9,interpolated +Y044d30,A/Brisbane/02/2018,1.291e+04,4,2489,interpolated +Y044d30,A/Brisbane/48/2022,986.9,3,1024,interpolated +Y044d30,A/California/07/2009,9227,4,1970,interpolated +Y044d30,A/Chester/5355/2022,2008,3,1087,interpolated +Y044d30,A/Cote_DIvoire/1448/2021,1.556e+04,3,1401,interpolated +Y044d30,A/England/220200318/2022,1.562e+04,3,628.9,interpolated +Y044d30,A/Ghana/138/2020,1.709e+04,3,2122,interpolated +Y044d30,A/Ghana/2080/2020,1.588e+04,3,145,interpolated +Y044d30,A/Hawaii/70/2019,1.379e+04,4,2671,interpolated +Y044d30,A/India-PUN-NIV328484/2021,1200,3,1314,interpolated +Y044d30,A/India-Pune-Nivcov2221170/2022,1416,2,227.5,interpolated +Y044d30,A/India/Pun-NIV312851/2021,900.8,3,130.9,interpolated +Y044d30,A/Michigan/19/2021,926.6,3,137.8,interpolated +Y044d30,A/Michigan/45/2015,1.37e+04,4,1383,interpolated +Y044d30,A/Newcastle/2/2022,859,3,128.5,interpolated +Y044d30,A/Niger/10217/2021,1.18e+04,3,840,interpolated +Y044d30,A/Nimes/871/2021,1.532e+04,3,102.6,interpolated +Y044d30,A/Norway/25089/2022,932.6,3,152.1,interpolated +Y044d30,A/Paris/30353/2021,8269,3,3439,interpolated +Y044d30,A/Paris/31196/2021,1.423e+04,3,1790,interpolated +Y044d30,A/Perth/1/2022,999.8,3,784.4,interpolated +Y044d30,A/SouthAfrica/R14850/2021,531.4,3,98.51,interpolated +Y044d30,A/SouthAfrica/R16462/2021,1.535e+04,3,253.1,interpolated +Y044d30,A/Sydney/43/2022,1640,3,519.7,interpolated +Y044d30,A/Togo/0274/2021,1.537e+04,3,4183,interpolated +Y044d30,A/Togo/0304/2021,9236,3,3618,interpolated +Y044d30,A/Togo/845/2020,1.697e+04,3,880.8,interpolated +Y044d30,A/Utah/27/2022,1205,3,175.5,interpolated +Y044d30,A/Washington/23/2020,4387,3,1251,interpolated +Y044d30,A/Wisconsin/588/2019,867.4,3,22.52,interpolated diff --git a/test_example/results/sera/Y044d30/titers_per_replicate.csv b/test_example/results/sera/Y044d30/titers_per_replicate.csv new file mode 100644 index 0000000..776c41e --- /dev/null +++ b/test_example/results/sera/Y044d30/titers_per_replicate.csv @@ -0,0 +1,111 @@ +serum,replicate,virus,nt50,nt50_bound +Y044d30,plate11-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,4168,interpolated +Y044d30,plate11-GACAGCAATGCATACA,A/Bangladesh/2221/2021,2125,interpolated +Y044d30,plate11-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,1180,interpolated +Y044d30,plate11-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,602.7,interpolated +Y044d30,plate11-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,467.6,interpolated +Y044d30,plate11-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,905.5,interpolated +Y044d30,plate11-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,1204,interpolated +Y044d30,plate11-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,1279,interpolated +Y044d30,plate11-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,1641,interpolated +Y044d30,plate11-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,1207,interpolated +Y044d30,plate11-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,5086,interpolated +Y044d30,plate11-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,1.252e+04,interpolated +Y044d30,plate11-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,1.654e+04,interpolated +Y044d30,plate11-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,1.443e+04,interpolated +Y044d30,plate11-GATCCGTACTTTGATT,A/Belgium/H0038/2022,1.442e+04,interpolated +Y044d30,plate11-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,1.337e+04,interpolated +Y044d30,plate11-TACCGTATAATTAAAA,A/Belgium/H0038/2022,1.508e+04,interpolated +Y044d30,plate11-ACGACATGATCAAACG,A/Brisbane/02/2018,1.025e+04,interpolated +Y044d30,plate11-ATCCGATTTAAAGGCA,A/Brisbane/02/2018,1.557e+04,interpolated +Y044d30,plate11-TAATAAGCCAGCAAGA,A/Brisbane/02/2018,7348,interpolated +Y044d30,plate11-TTGGGCACTAAATTAA,A/Brisbane/02/2018,1.832e+04,interpolated +Y044d30,plate11-CCCTATGCTGCGTATT,A/Brisbane/48/2022,986.9,interpolated +Y044d30,plate11-GAGCTCTAAAGCAACA,A/Brisbane/48/2022,804.9,interpolated +Y044d30,plate11-TTATGATCTAAACAGA,A/Brisbane/48/2022,3965,interpolated +Y044d30,plate11-CATGTGAATTCGCCCA,A/California/07/2009,7484,interpolated +Y044d30,plate11-CCTTTCTCAAAACATA,A/California/07/2009,1.558e+04,interpolated +Y044d30,plate11-CGCCTAATGTTAATAA,A/California/07/2009,7087,interpolated +Y044d30,plate11-GACACAGAACCCATGC,A/California/07/2009,1.097e+04,interpolated +Y044d30,plate11-AAAAAACGCATGTAGA,A/Chester/5355/2022,2008,interpolated +Y044d30,plate11-CCTCAAAATAACAAGC,A/Chester/5355/2022,792.3,interpolated +Y044d30,plate11-TCATATAAAGAAAAGG,A/Chester/5355/2022,4487,interpolated +Y044d30,plate11-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,1.592e+04,interpolated +Y044d30,plate11-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,1.155e+04,interpolated +Y044d30,plate11-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,1.556e+04,interpolated +Y044d30,plate11-CGTAATACATTTAAGA,A/England/220200318/2022,1.485e+04,interpolated +Y044d30,plate11-GACCAACTGTGGTACA,A/England/220200318/2022,1.562e+04,interpolated +Y044d30,plate11-GCTGCGCCTAACATAA,A/England/220200318/2022,1.7e+04,interpolated +Y044d30,plate11-CCAGTTCCCTTCGATG,A/Ghana/138/2020,1.709e+04,interpolated +Y044d30,plate11-GACTATGGTCTAAAAA,A/Ghana/138/2020,2.211e+04,interpolated +Y044d30,plate11-TAAGCCATAAATCAAT,A/Ghana/138/2020,1.495e+04,interpolated +Y044d30,plate11-CAGCAAAAGCATCACC,A/Ghana/2080/2020,1.609e+04,interpolated +Y044d30,plate11-GCAATCCCGCAATTTG,A/Ghana/2080/2020,1.559e+04,interpolated +Y044d30,plate11-GTAGTGCATCATTGAT,A/Ghana/2080/2020,1.588e+04,interpolated +Y044d30,plate11-ACATGAATTCAGACGG,A/Hawaii/70/2019,1.726e+04,interpolated +Y044d30,plate11-AGTAAACATGCATTGG,A/Hawaii/70/2019,5022,interpolated +Y044d30,plate11-ATAGAATCGCAAATTA,A/Hawaii/70/2019,1.243e+04,interpolated +Y044d30,plate11-TGGAATCGTCACCGAT,A/Hawaii/70/2019,1.515e+04,interpolated +Y044d30,plate11-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,5037,interpolated +Y044d30,plate11-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,1200,interpolated +Y044d30,plate11-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,995.6,interpolated +Y044d30,plate11-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,1643,interpolated +Y044d30,plate11-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,1188,interpolated +Y044d30,plate11-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,900.8,interpolated +Y044d30,plate11-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,891.8,interpolated +Y044d30,plate11-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,1289,interpolated +Y044d30,plate11-AACGTTAACAAATGAA,A/Michigan/19/2021,798.8,interpolated +Y044d30,plate11-AGAGAAAAAACAGTGA,A/Michigan/19/2021,926.6,interpolated +Y044d30,plate11-TAATGAGCTTTATGGT,A/Michigan/19/2021,1261,interpolated +Y044d30,plate11-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,1.405e+04,interpolated +Y044d30,plate11-CACCTAGGATCGCACT,A/Michigan/45/2015,1.336e+04,interpolated +Y044d30,plate11-TGAGGATAATCACAAG,A/Michigan/45/2015,1.622e+04,interpolated +Y044d30,plate11-TTGAAAAAATCATAAA,A/Michigan/45/2015,9578,interpolated +Y044d30,plate11-CAAATATATCTTCATG,A/Newcastle/2/2022,859,interpolated +Y044d30,plate11-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,749.6,interpolated +Y044d30,plate11-TTCACTAAGATTTCAT,A/Newcastle/2/2022,1178,interpolated +Y044d30,plate11-AAATAAGTACGCAAAT,A/Niger/10217/2021,1.18e+04,interpolated +Y044d30,plate11-CATCAACCGCCATTTC,A/Niger/10217/2021,1.386e+04,interpolated +Y044d30,plate11-GAACGATTGTAATTTT,A/Niger/10217/2021,1.105e+04,interpolated +Y044d30,plate11-ACCTTACTAAATCCTG,A/Nimes/871/2021,1.54e+04,interpolated +Y044d30,plate11-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,1.506e+04,interpolated +Y044d30,plate11-TAATTACATTGCGGTT,A/Nimes/871/2021,1.532e+04,interpolated +Y044d30,plate11-CGGATAAAAATGATAT,A/Norway/25089/2022,1111,interpolated +Y044d30,plate11-GACTCAATAATCACAC,A/Norway/25089/2022,592.6,interpolated +Y044d30,plate11-TGGAAAAGATGTAATA,A/Norway/25089/2022,932.6,interpolated +Y044d30,plate11-ACATAAGAACCCTATA,A/Paris/30353/2021,5745,interpolated +Y044d30,plate11-ACATTTCCCTCGATAT,A/Paris/30353/2021,8269,interpolated +Y044d30,plate11-GTTTGACAATCACTAC,A/Paris/30353/2021,1.709e+04,interpolated +Y044d30,plate11-AAACTAAAAGCAAGGG,A/Paris/31196/2021,1.423e+04,interpolated +Y044d30,plate11-AATAAGTATACGGGAT,A/Paris/31196/2021,1.29e+04,interpolated +Y044d30,plate11-AGCAGCCTGAAAATAT,A/Paris/31196/2021,1.881e+04,interpolated +Y044d30,plate11-AGCCCCGTGAGAAGCA,A/Perth/1/2022,3274,interpolated +Y044d30,plate11-CTGCACGAGAGACTTC,A/Perth/1/2022,999.8,interpolated +Y044d30,plate11-TTGGGGAAATATATAA,A/Perth/1/2022,849.3,interpolated +Y044d30,plate11-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,531.4,interpolated +Y044d30,plate11-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,731.1,interpolated +Y044d30,plate11-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,391.6,interpolated +Y044d30,plate11-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,1.501e+04,interpolated +Y044d30,plate11-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,1.535e+04,interpolated +Y044d30,plate11-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,1.588e+04,interpolated +Y044d30,plate11-CTATTAATCATGCAAA,A/Sydney/43/2022,2766,interpolated +Y044d30,plate11-TACGGACATTCTTAAC,A/Sydney/43/2022,986.4,interpolated +Y044d30,plate11-TAGTATAATAGAGCAG,A/Sydney/43/2022,1640,interpolated +Y044d30,plate11-AACGAATGAATTTCTT,A/Togo/0274/2021,1.537e+04,interpolated +Y044d30,plate11-GTAACATTATACGATT,A/Togo/0274/2021,2.757e+04,interpolated +Y044d30,plate11-TAGCAGATGTATCAAT,A/Togo/0274/2021,1.47e+04,interpolated +Y044d30,plate11-AACTCTAAAGATATAA,A/Togo/0304/2021,1.787e+04,interpolated +Y044d30,plate11-AGAGATAATAACAAAA,A/Togo/0304/2021,9236,interpolated +Y044d30,plate11-GAAGAATGGTTTTCTG,A/Togo/0304/2021,5686,interpolated +Y044d30,plate11-AGGTCAAGACCACAGG,A/Togo/845/2020,1.609e+04,interpolated +Y044d30,plate11-GCATGGATCCTTTACT,A/Togo/845/2020,1.697e+04,interpolated +Y044d30,plate11-TTACCGTCTACGCATA,A/Togo/845/2020,1.906e+04,interpolated +Y044d30,plate11-ACAATGTGACTCACCC,A/Utah/27/2022,1205,interpolated +Y044d30,plate11-TAAATAACTCGTATTT,A/Utah/27/2022,1059,interpolated +Y044d30,plate11-TCCTTGTAATTCAACT,A/Utah/27/2022,1643,interpolated +Y044d30,plate11-ACGGAATCCCCTGAGA,A/Washington/23/2020,4387,interpolated +Y044d30,plate11-GAACTGGCGTCAATCA,A/Washington/23/2020,4864,interpolated +Y044d30,plate11-GGATAAGAAAACTACT,A/Washington/23/2020,895.9,interpolated +Y044d30,plate11-AGTCCTATCCTCAAAT,A/Wisconsin/588/2019,867.4,interpolated +Y044d30,plate11-GAAGAAACTATAACCA,A/Wisconsin/588/2019,809,interpolated +Y044d30,plate11-TATATTAGTAACATAA,A/Wisconsin/588/2019,883,interpolated diff --git a/test_example/results/sera/Y154d182/titers_median.csv b/test_example/results/sera/Y154d182/titers_median.csv new file mode 100644 index 0000000..d1088e5 --- /dev/null +++ b/test_example/results/sera/Y154d182/titers_median.csv @@ -0,0 +1,37 @@ +serum,virus,nt50,n_replicates,nt50_stderr,nt50_bound +Y154d182,A/Bangladesh/2221/2021,191.3,3,2.345,interpolated +Y154d182,A/Bangladesh/3210810034/2021,200.9,2,7.3,interpolated +Y154d182,A/Bangladesh/8002/2021,203,3,6.583,interpolated +Y154d182,A/Bangladesh/8036/2021,208.6,3,13.99,interpolated +Y154d182,A/Belgium/H0017/2022,1717,3,533.9,interpolated +Y154d182,A/Belgium/H0038/2022,3018,3,340.4,interpolated +Y154d182,A/Brisbane/02/2018,3786,4,443.6,interpolated +Y154d182,A/Brisbane/48/2022,198.9,3,3.967,interpolated +Y154d182,A/California/07/2009,4098,4,650.2,interpolated +Y154d182,A/Chester/5355/2022,201.6,3,7.105,interpolated +Y154d182,A/Cote_DIvoire/1448/2021,3124,3,520.3,interpolated +Y154d182,A/England/220200318/2022,2513,3,663.2,interpolated +Y154d182,A/Ghana/138/2020,2794,3,294.1,interpolated +Y154d182,A/Ghana/2080/2020,2762,3,665.4,interpolated +Y154d182,A/Hawaii/70/2019,3675,4,496.1,interpolated +Y154d182,A/India-PUN-NIV328484/2021,239.5,3,40.3,interpolated +Y154d182,A/India-Pune-Nivcov2221170/2022,170.2,2,1.3,interpolated +Y154d182,A/India/Pun-NIV312851/2021,218.8,3,76.96,interpolated +Y154d182,A/Michigan/19/2021,208.9,3,72.27,interpolated +Y154d182,A/Michigan/45/2015,5578,4,1182,interpolated +Y154d182,A/Newcastle/2/2022,215.6,3,40.11,interpolated +Y154d182,A/Niger/10217/2021,2938,3,423,interpolated +Y154d182,A/Nimes/871/2021,3441,3,568.7,interpolated +Y154d182,A/Norway/25089/2022,191.2,3,66.9,interpolated +Y154d182,A/Paris/30353/2021,2306,3,307.3,interpolated +Y154d182,A/Paris/31196/2021,5608,3,1716,interpolated +Y154d182,A/Perth/1/2022,259.4,3,24.65,interpolated +Y154d182,A/SouthAfrica/R14850/2021,200.2,3,5.32,interpolated +Y154d182,A/SouthAfrica/R16462/2021,3200,3,785.8,interpolated +Y154d182,A/Sydney/43/2022,237.9,3,46.09,interpolated +Y154d182,A/Togo/0274/2021,3474,3,600.4,interpolated +Y154d182,A/Togo/0304/2021,2602,3,631.4,interpolated +Y154d182,A/Togo/845/2020,1815,3,265.8,interpolated +Y154d182,A/Utah/27/2022,236.2,3,16.55,interpolated +Y154d182,A/Washington/23/2020,620.8,3,17.26,interpolated +Y154d182,A/Wisconsin/588/2019,1153,3,295.6,interpolated diff --git a/test_example/results/sera/Y154d182/titers_per_replicate.csv b/test_example/results/sera/Y154d182/titers_per_replicate.csv new file mode 100644 index 0000000..e251162 --- /dev/null +++ b/test_example/results/sera/Y154d182/titers_per_replicate.csv @@ -0,0 +1,111 @@ +serum,replicate,virus,nt50,nt50_bound +Y154d182,plate2-AAGAGAAATATTCGCT,A/Bangladesh/2221/2021,197.9,interpolated +Y154d182,plate2-GACAGCAATGCATACA,A/Bangladesh/2221/2021,190.5,interpolated +Y154d182,plate2-GATAGAAATACCAGGA,A/Bangladesh/2221/2021,191.3,interpolated +Y154d182,plate2-AACTATAGATCTAGAA,A/Bangladesh/3210810034/2021,193.6,interpolated +Y154d182,plate2-ACAAAAGTACCTCTAC,A/Bangladesh/3210810034/2021,208.2,interpolated +Y154d182,plate2-AGTGTCCCTAAGAGGC,A/Bangladesh/8002/2021,197.2,interpolated +Y154d182,plate2-GCAACGCCAAATAATT,A/Bangladesh/8002/2021,203,interpolated +Y154d182,plate2-TCTGCTAAACTAAGTA,A/Bangladesh/8002/2021,219.2,interpolated +Y154d182,plate2-ACGGGGCCCAGGTAAT,A/Bangladesh/8036/2021,208.6,interpolated +Y154d182,plate2-ATACCTCAACCTTGAA,A/Bangladesh/8036/2021,192.1,interpolated +Y154d182,plate2-CAGTTCTGCGACCAGC,A/Bangladesh/8036/2021,239.8,interpolated +Y154d182,plate2-AATGAAAGTTAGCATT,A/Belgium/H0017/2022,3104,interpolated +Y154d182,plate2-ATGTCCATAAAAAATA,A/Belgium/H0017/2022,1351,interpolated +Y154d182,plate2-GTAAAGCAAATCCATT,A/Belgium/H0017/2022,1717,interpolated +Y154d182,plate2-GATCCGTACTTTGATT,A/Belgium/H0038/2022,2574,interpolated +Y154d182,plate2-GCCGGAGGGCATTTTC,A/Belgium/H0038/2022,3742,interpolated +Y154d182,plate2-TACCGTATAATTAAAA,A/Belgium/H0038/2022,3018,interpolated +Y154d182,plate2-ACGACATGATCAAACG,A/Brisbane/02/2018,4977,interpolated +Y154d182,plate2-ATCCGATTTAAAGGCA,A/Brisbane/02/2018,3002,interpolated +Y154d182,plate2-TAATAAGCCAGCAAGA,A/Brisbane/02/2018,3356,interpolated +Y154d182,plate2-TTGGGCACTAAATTAA,A/Brisbane/02/2018,4216,interpolated +Y154d182,plate2-CCCTATGCTGCGTATT,A/Brisbane/48/2022,207.4,interpolated +Y154d182,plate2-GAGCTCTAAAGCAACA,A/Brisbane/48/2022,198.9,interpolated +Y154d182,plate2-TTATGATCTAAACAGA,A/Brisbane/48/2022,193.8,interpolated +Y154d182,plate2-CATGTGAATTCGCCCA,A/California/07/2009,2078,interpolated +Y154d182,plate2-CCTTTCTCAAAACATA,A/California/07/2009,4930,interpolated +Y154d182,plate2-CGCCTAATGTTAATAA,A/California/07/2009,3527,interpolated +Y154d182,plate2-GACACAGAACCCATGC,A/California/07/2009,4670,interpolated +Y154d182,plate2-AAAAAACGCATGTAGA,A/Chester/5355/2022,214.6,interpolated +Y154d182,plate2-CCTCAAAATAACAAGC,A/Chester/5355/2022,190,interpolated +Y154d182,plate2-TCATATAAAGAAAAGG,A/Chester/5355/2022,201.6,interpolated +Y154d182,plate2-GTCCGTTGATAAAGAG,A/Cote_DIvoire/1448/2021,3124,interpolated +Y154d182,plate2-GTTAAACGATCTATAG,A/Cote_DIvoire/1448/2021,3555,interpolated +Y154d182,plate2-TCGAGAACACCCATAA,A/Cote_DIvoire/1448/2021,1824,interpolated +Y154d182,plate2-CGTAATACATTTAAGA,A/England/220200318/2022,2513,interpolated +Y154d182,plate2-GACCAACTGTGGTACA,A/England/220200318/2022,1725,interpolated +Y154d182,plate2-GCTGCGCCTAACATAA,A/England/220200318/2022,3988,interpolated +Y154d182,plate2-CCAGTTCCCTTCGATG,A/Ghana/138/2020,2794,interpolated +Y154d182,plate2-GACTATGGTCTAAAAA,A/Ghana/138/2020,2609,interpolated +Y154d182,plate2-TAAGCCATAAATCAAT,A/Ghana/138/2020,3569,interpolated +Y154d182,plate2-CAGCAAAAGCATCACC,A/Ghana/2080/2020,1729,interpolated +Y154d182,plate2-GCAATCCCGCAATTTG,A/Ghana/2080/2020,4030,interpolated +Y154d182,plate2-GTAGTGCATCATTGAT,A/Ghana/2080/2020,2762,interpolated +Y154d182,plate2-ACATGAATTCAGACGG,A/Hawaii/70/2019,3948,interpolated +Y154d182,plate2-AGTAAACATGCATTGG,A/Hawaii/70/2019,1880,interpolated +Y154d182,plate2-ATAGAATCGCAAATTA,A/Hawaii/70/2019,3402,interpolated +Y154d182,plate2-TGGAATCGTCACCGAT,A/Hawaii/70/2019,4012,interpolated +Y154d182,plate2-GATCTAATAATACGGC,A/India-PUN-NIV328484/2021,239.5,interpolated +Y154d182,plate2-TCTGTTCCGGCCCGAA,A/India-PUN-NIV328484/2021,202.8,interpolated +Y154d182,plate2-TTGTCCCGAGACAACA,A/India-PUN-NIV328484/2021,337.8,interpolated +Y154d182,plate2-AAATCTACCGCATTAT,A/India-Pune-Nivcov2221170/2022,168.9,interpolated +Y154d182,plate2-CGTTTAAACAATGAAG,A/India-Pune-Nivcov2221170/2022,171.5,interpolated +Y154d182,plate2-ACAGCAAATACTCACA,A/India/Pun-NIV312851/2021,210.3,interpolated +Y154d182,plate2-CAAGAACCCAAATATA,A/India/Pun-NIV312851/2021,218.8,interpolated +Y154d182,plate2-GTAGCTATAACTAATA,A/India/Pun-NIV312851/2021,445.3,interpolated +Y154d182,plate2-AACGTTAACAAATGAA,A/Michigan/19/2021,104.2,interpolated +Y154d182,plate2-AGAGAAAAAACAGTGA,A/Michigan/19/2021,353.5,interpolated +Y154d182,plate2-TAATGAGCTTTATGGT,A/Michigan/19/2021,208.9,interpolated +Y154d182,plate2-ACAAAGTCTCGAGAAG,A/Michigan/45/2015,5710,interpolated +Y154d182,plate2-CACCTAGGATCGCACT,A/Michigan/45/2015,5446,interpolated +Y154d182,plate2-TGAGGATAATCACAAG,A/Michigan/45/2015,9666,interpolated +Y154d182,plate2-TTGAAAAAATCATAAA,A/Michigan/45/2015,4214,interpolated +Y154d182,plate2-CAAATATATCTTCATG,A/Newcastle/2/2022,321.4,interpolated +Y154d182,plate2-GCCCAAGTAGGTGCAA,A/Newcastle/2/2022,215.6,interpolated +Y154d182,plate2-TTCACTAAGATTTCAT,A/Newcastle/2/2022,190.5,interpolated +Y154d182,plate2-AAATAAGTACGCAAAT,A/Niger/10217/2021,2938,interpolated +Y154d182,plate2-CATCAACCGCCATTTC,A/Niger/10217/2021,1888,interpolated +Y154d182,plate2-GAACGATTGTAATTTT,A/Niger/10217/2021,3298,interpolated +Y154d182,plate2-ACCTTACTAAATCCTG,A/Nimes/871/2021,3441,interpolated +Y154d182,plate2-GTTCCTTTAAGCCAAA,A/Nimes/871/2021,2436,interpolated +Y154d182,plate2-TAATTACATTGCGGTT,A/Nimes/871/2021,4406,interpolated +Y154d182,plate2-CGGATAAAAATGATAT,A/Norway/25089/2022,188.6,interpolated +Y154d182,plate2-GACTCAATAATCACAC,A/Norway/25089/2022,191.2,interpolated +Y154d182,plate2-TGGAAAAGATGTAATA,A/Norway/25089/2022,390.6,interpolated +Y154d182,plate2-ACATAAGAACCCTATA,A/Paris/30353/2021,1726,interpolated +Y154d182,plate2-ACATTTCCCTCGATAT,A/Paris/30353/2021,2789,interpolated +Y154d182,plate2-GTTTGACAATCACTAC,A/Paris/30353/2021,2306,interpolated +Y154d182,plate2-AAACTAAAAGCAAGGG,A/Paris/31196/2021,5608,interpolated +Y154d182,plate2-AATAAGTATACGGGAT,A/Paris/31196/2021,7768,interpolated +Y154d182,plate2-AGCAGCCTGAAAATAT,A/Paris/31196/2021,1891,interpolated +Y154d182,plate2-AGCCCCGTGAGAAGCA,A/Perth/1/2022,204.5,interpolated +Y154d182,plate2-CTGCACGAGAGACTTC,A/Perth/1/2022,259.4,interpolated +Y154d182,plate2-TTGGGGAAATATATAA,A/Perth/1/2022,288.6,interpolated +Y154d182,plate2-AACTCCGCAGACACTG,A/SouthAfrica/R14850/2021,200.2,interpolated +Y154d182,plate2-GAGACGTACGAAATTA,A/SouthAfrica/R14850/2021,185.7,interpolated +Y154d182,plate2-TACTCAACAAGATAAA,A/SouthAfrica/R14850/2021,202.8,interpolated +Y154d182,plate2-CACCATTAAAGAGGTA,A/SouthAfrica/R16462/2021,5285,interpolated +Y154d182,plate2-CGGCGTATCGTTCACA,A/SouthAfrica/R16462/2021,3200,interpolated +Y154d182,plate2-CTAGCAGATTGTATAA,A/SouthAfrica/R16462/2021,2727,interpolated +Y154d182,plate2-CTATTAATCATGCAAA,A/Sydney/43/2022,198.1,interpolated +Y154d182,plate2-TACGGACATTCTTAAC,A/Sydney/43/2022,237.9,interpolated +Y154d182,plate2-TAGTATAATAGAGCAG,A/Sydney/43/2022,351.9,interpolated +Y154d182,plate2-AACGAATGAATTTCTT,A/Togo/0274/2021,3721,interpolated +Y154d182,plate2-GTAACATTATACGATT,A/Togo/0274/2021,1809,interpolated +Y154d182,plate2-TAGCAGATGTATCAAT,A/Togo/0274/2021,3474,interpolated +Y154d182,plate2-AACTCTAAAGATATAA,A/Togo/0304/2021,2602,interpolated +Y154d182,plate2-AGAGATAATAACAAAA,A/Togo/0304/2021,4203,interpolated +Y154d182,plate2-GAAGAATGGTTTTCTG,A/Togo/0304/2021,2112,interpolated +Y154d182,plate2-AGGTCAAGACCACAGG,A/Togo/845/2020,2396,interpolated +Y154d182,plate2-GCATGGATCCTTTACT,A/Togo/845/2020,1487,interpolated +Y154d182,plate2-TTACCGTCTACGCATA,A/Togo/845/2020,1815,interpolated +Y154d182,plate2-ACAATGTGACTCACCC,A/Utah/27/2022,236.2,interpolated +Y154d182,plate2-TAAATAACTCGTATTT,A/Utah/27/2022,275.2,interpolated +Y154d182,plate2-TCCTTGTAATTCAACT,A/Utah/27/2022,219.3,interpolated +Y154d182,plate2-ACGGAATCCCCTGAGA,A/Washington/23/2020,591,interpolated +Y154d182,plate2-GAACTGGCGTCAATCA,A/Washington/23/2020,620.8,interpolated +Y154d182,plate2-GGATAAGAAAACTACT,A/Washington/23/2020,650.8,interpolated +Y154d182,plate2-AGTCCTATCCTCAAAT,A/Wisconsin/588/2019,1624,interpolated +Y154d182,plate2-GAAGAAACTATAACCA,A/Wisconsin/588/2019,1153,interpolated +Y154d182,plate2-TATATTAGTAACATAA,A/Wisconsin/588/2019,601.2,interpolated diff --git a/test_example/results/sera/qc_serum_titers_summary.txt b/test_example/results/sera/qc_serum_titers_summary.txt new file mode 100644 index 0000000..4648641 --- /dev/null +++ b/test_example/results/sera/qc_serum_titers_summary.txt @@ -0,0 +1,6 @@ +M099d0 serum passed all QC +M099d30 serum_titers QC failures, see results/sera/M099d30/serum_titers_M099d30.html for details + max_fold_change_from_median +Y044d30 serum_titers QC failures, see results/sera/Y044d30/serum_titers_Y044d30.html for details + max_fold_change_from_median +Y154d182 serum passed all QC \ No newline at end of file diff --git a/test_example/results/sera/sera_by_plate.csv b/test_example/results/sera/sera_by_plate.csv new file mode 100644 index 0000000..c305656 --- /dev/null +++ b/test_example/results/sera/sera_by_plate.csv @@ -0,0 +1,5 @@ +serum,plates +M099d0,plate11;plate2 +M099d30,plate11;plate2 +Y044d30,plate11 +Y154d182,plate2