Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Immune Escape Ranking #227

Open
ktmeaton opened this issue Jan 25, 2023 · 1 comment
Open

Immune Escape Ranking #227

ktmeaton opened this issue Jan 25, 2023 · 1 comment

Comments

@ktmeaton
Copy link
Owner

ktmeaton commented Jan 25, 2023 •
edited
Loading

v0.7.0 (2023-02-23)

lineage rbd_level immune_escape ace2_binding
XBL 7 0.9070 1.0124
XBB.1.5 7 0.9070 1.0124
XBB 7 0.9070 0.4069
XBN 7 0.9070 0.4069
XBB.1 7 0.9070 0.4069
XBK 6 0.8366 1.0428
XBF 6 0.8366 1.0428
XBD 5 0.6339 0.4677
XBH 5 0.6339 0.4677
XBP 5 0.6307 0.6640
XBM 4 0.6014 0.6697
XBE 4 0.6014 0.6697
XBG 4 0.6014 0.6697
XBJ 5 0.5925 1.0634
XBC.1 4 0.5283 0.7927
XAY.1 4 0.5283 0.6144
XAY.2 4 0.5283 0.6144
XAY 4 0.5283 0.6144
XAS 3 0.3863 0.5583
XAZ 3 0.3863 0.5583
XAN 3 0.3863 0.5583
XAJ 3 0.3863 0.5583
XAV 3 0.3434 0.4963
XBC.2 3 0.3263 0.6872
XBA 3 0.3155 0.2022
XAK 2 0.2769 1.3052
XAW 4 0.2120 1.0223
XC 2 0.1935 -2.6545
XD 1 0.1528 -0.0291
XJ 0 0.0168 0.0082
XAG 0 0.0021 0.0419
XH 0 0.0002 -0.0078
XB 1 NA NA
XS 1 NA NA
XF 1 NA NA
XA 1 NA NA
XP 1 NA NA
XK 0 -0.0001 0.1551
XAE 0 -0.0001 0.0660
XAM 0 -0.0001 0.0583
XL 0 -0.0001 0.0000
XAR 0 -0.0001 0.0000
XAT 0 -0.0001 0.0000
XE 0 -0.0001 0.0000
XW 0 -0.0001 0.0000
XAC 0 -0.0001 0.0000
XAH 0 -0.0001 0.0000
XAQ 0 -0.0001 0.0000
XZ 0 -0.0001 0.0000
XAP 0 -0.0001 0.0000
XR 0 -0.0001 0.0000
XM 0 -0.0001 0.0000
XY 0 -0.0001 0.0000
XQ 0 -0.0001 0.0000
XT 0 -0.0001 0.0000
XG 0 -0.0001 0.0000
XAL 0 -0.0001 0.0000
XAF 0 -0.0001 0.0000
XV 0 -0.0001 0.0000
XN 0 -0.0001 0.0000
XAU 0 -0.0001 -0.0173
XAA 0 -0.0001 -0.0173
XAB 0 -0.0001 -0.0173
XU 0 -0.0001 -0.0191
XAD 0 -0.0001 -0.0345

Command to generate the from the GISAID controls:

csvtk cut -t -f "lineage,rbd_level,immune_escape,ace2_binding" results/controls-gisaid/linelists/lineages.tsv \
  | csvtk sort -t -k "immune_escape:nr,ace2_binding:nr" \
  | csvtk uniq -t -f "lineage" \
  | csvtk round -t -f "immune_escape,ace2_binding" -n 4 \
  | csvtk csv2md -t
@ktmeaton
Copy link
Owner Author

ktmeaton commented Feb 23, 2023 •
edited
Loading

v0.7.0 (2023-01-25)

lineage rbd_level immune_escape ace2_binding
XBL 7 0.9070 1.0124
XBB.1.5 7 0.9070 1.0124
XBB 7 0.9070 0.4069
XBB.1 7 0.9070 0.4069
XBF 6 0.8366 1.0428
XBK 6 0.8366 1.0428
XBD 5 0.6339 0.4677
XBH 5 0.6339 0.4677
XBM 4 0.6014 0.6697
XBG 4 0.6014 0.6697
XBE 4 0.6014 0.6697
XBJ 5 0.5925 1.0634
XBJ-like 4 0.5515 0.1235
XBC.1 4 0.5283 0.7927
XAY 4 0.5283 0.6144
XAY.2 4 0.5283 0.6144
XAY.1 4 0.5283 0.6144
XAN 3 0.3863 0.5583
XAS 3 0.3863 0.5583
XAZ 3 0.3863 0.5583
XAJ 3 0.3863 0.5583
XAV 3 0.3434 0.4963
XBC.2 3 0.3263 0.6872
XBA 3 0.3155 0.2022
XAK 2 0.2769 1.3052
XAW 4 0.2120 1.0223
XC 2 0.1935 -2.6545
XD 1 0.1528 -0.0291
XJ 0 0.0168 0.0082
XAG 0 0.0021 0.0419
XH 0 0.0002 -0.0078
XP 1 NA NA
XA 1 NA NA
XB 1 NA NA
XF 1 NA NA
XS 1 NA NA
XK 0 -0.0001 0.1551
XAE 0 -0.0001 0.0660
XAM 0 -0.0001 0.0583
XAL 0 -0.0001 0.0000
XAT 0 -0.0001 0.0000
XAH 0 -0.0001 0.0000
XAP 0 -0.0001 0.0000
XAF 0 -0.0001 0.0000
XY 0 -0.0001 0.0000
XZ 0 -0.0001 0.0000
XAR 0 -0.0001 0.0000
XV 0 -0.0001 0.0000
XR 0 -0.0001 0.0000
XM 0 -0.0001 0.0000
XAQ 0 -0.0001 0.0000
XG 0 -0.0001 0.0000
XQ 0 -0.0001 0.0000
XW 0 -0.0001 0.0000
XAC 0 -0.0001 0.0000
XE 0 -0.0001 0.0000
XN 0 -0.0001 0.0000
XL 0 -0.0001 0.0000
XT 0 -0.0001 0.0000
XAA 0 -0.0001 -0.0173
XAU 0 -0.0001 -0.0173
XAB 0 -0.0001 -0.0173
XU 0 -0.0001 -0.0191
XAD 0 -0.0001 -0.0345

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@ktmeaton