diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.bed b/2022_Kennett_Belize/2022_Kennett_Belize.bed new file mode 100644 index 0000000..d2786ad --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3098dc9ed4bb3532409e0b7327b856a9c70960b2c823ccbfed1aa6bf02ee2d8b +size 7398081 diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.bib b/2022_Kennett_Belize/2022_Kennett_Belize.bib new file mode 100644 index 0000000..532dab0 --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.bib @@ -0,0 +1,23 @@ +@ARTICLE{2022KennettNatureCommunications, + title = "{South-to-north migration preceded the advent of intensive + farming in the Maya region}", + author = "Kennett, Douglas J and Lipson, Mark and Prufer, Keith M and + Mora-Marín, David and George, Richard J and Rohland, Nadin and + Robinson, Mark and Trask, Willa R and Edgar, Heather H J and + Hill, Ethan C and Ray, Erin E and Lynch, Paige and Moes, Emily + and O'Donnell, Lexi and Harper, Thomas K and Kate, Emily J and + Ramos, Josue and Morris, John and Gutierrez, Said M and Ryan, + Timothy M and Culleton, Brendan J and Awe, Jaime J and Reich, + David", + journal = "Nature Communications", + publisher = "Nature Publishing Group", + volume = 13, + number = 1, + pages = "1--10", + month = mar, + year = 2022, + url = "https://www.nature.com/articles/s41467-022-29158-y", + doi = "10.1038/s41467-022-29158-y", + issn = "2041-1723,2041-1723", + language = "en" +} diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.bim b/2022_Kennett_Belize/2022_Kennett_Belize.bim new file mode 100644 index 0000000..384f3bc --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.bim @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3d3c4aaa95fc68acd08d9695f14fc8e777d6078d59a2ca64bdaeb770d135d4e +size 43313767 diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.fam b/2022_Kennett_Belize/2022_Kennett_Belize.fam new file mode 100644 index 0000000..1ede724 --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.fam @@ -0,0 +1,23 @@ +Mayahak_Cab_Pek I13267_MNT 0 0 2 0 +Mayahak_Cab_Pek I13268_MNT 0 0 1 0 +Mayahak_Cab_Pek I13268_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I19167_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I19169_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I19170_ss_MNT 0 0 2 0 +Saki_Tzul I19942_ss_MNT 0 0 2 0 +Saki_Tzul I19944_ss_MNT 0 0 1 0 +Saki_Tzul I19950_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I20428_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I24540_MNT 0 0 2 0 +Mayahak_Cab_Pek I24541_MNT 0 0 1 0 +Mayahak_Cab_Pek I24542_MNT 0 0 2 0 +Unknown I3422_MNT 0 0 0 0 +Mayahak_Cab_Pek I3442_MNT 0 0 1 0 +Mayahak_Cab_Pek I5454_MNT 0 0 1 0 +Mayahak_Cab_Pek I5455_MNT 0 0 1 0 +Mayahak_Cab_Pek I6235_MNT 0 0 1 0 +Saki_Tzul I6236_MNT 0 0 2 0 +Mayahak_Cab_Pek I7543_MNT 0 0 1 0 +Mayahak_Cab_Pek I7543_ss_MNT 0 0 1 0 +Mayahak_Cab_Pek I7544_MNT 0 0 2 0 +Mayahak_Cab_Pek I8041_MNT 0 0 1 0 diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.janno b/2022_Kennett_Belize/2022_Kennett_Belize.janno new file mode 100644 index 0000000..13422af --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.janno @@ -0,0 +1,24 @@ +Poseidon_ID Genetic_Sex Group_Name Relation_To Relation_Degree Relation_Note Collection_ID Country Country_ISO Location Site Latitude Longitude Date_Type Date_C14_Labnr Date_C14_Uncal_BP Date_C14_Uncal_BP_Err Date_Note MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Library_Names Capture_Type UDG Library_Built Genotype_Ploidy Data_Preparation_Pipeline_URL Nr_SNPs Damage Contamination Contamination_Err Contamination_Meas Contamination_Note Genetic_Source_Accession_IDs Publication Eager_ID Main_ID RateErrX RateErrY RateX RateY +I13267_MNT F Mayahak_Cab_Pek n/a n/a n/a MHCP.17.1.7 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-3607;UCIAMS-228026 4725;4775 25;45 n/a C1c n/a bone_petrous 2 I13267.mt;I13267.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 778420 0.232728729768832 0.220769 2.003269e-12 ANGSD[v0.935] Nr Snps (per library): 0;7581. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293359;ERR7735786;ERR7735765 2022KennettNatureCommunications I13267 I13267 0.0027175168019670003 0.00028348542545400003 0.76262810751771 0.005633710837733 +I13268_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.17.1.8 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4290 8565 45 enamel carbonate C1b Q1a2a1a1 bone_petrous 1 I13268.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 0 0.418141592920354 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293354;ERR7735781 2022KennettNatureCommunications I13268 I13268 0.0 0.0 0.0 0.0 +I13268_ss_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.17.1.8 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4290 8565 45 enamel carbonate C1b Q1a2a1a1 bone_petrous 1 I13268.1240k OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 108154 0.461117201393457 n/a n/a n/a Nr Snps (per library): 78. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293354;ERR7735760 2022KennettNatureCommunications I13268_ss I13268 0.007424654484514 0.009530526384593 0.44159656188260704 0.480819781223132 +I19167_ss_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.17.2.11a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4582 4330 20 n/a n/a n/a bone_petrous 2 I19167.mt;I19167.1240k OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 22739 0.45807954833289666 n/a n/a n/a Nr Snps (per library): 0;9. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293363;ERR7735790;ERR7735769 2022KennettNatureCommunications I19167_ss I19167 0.016367992913651 0.022926497382377002 0.42696625576615205 0.5521000917133151 +I19169_ss_MNT M Mayahak_Cab_Pek I19170_ss_MNT first n/a MHCP.17.1.c1 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4800 7900 35 n/a D4h3a n/a bone_petrous 2 I19169.1240k;I19169.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 46914 0.4282981558767512 n/a n/a n/a Nr Snps (per library): 11;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293355;ERR7735761;ERR7735782 2022KennettNatureCommunications I19169_ss I19169 0.011195078578139001 0.014254652187201 0.42101226124024205 0.451037252592052 +I19170_ss_MNT F Mayahak_Cab_Pek I19169_ss_MNT first n/a MHCP.17.1.1b Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 n/a n/a n/a n/a Undated, but first-degree relative of I19169 D4h3a5 n/a bone_petrous 2 I19170.1240k;I19170.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 46551 0.45462536537462594 n/a n/a n/a Nr Snps (per library): 53;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293356;ERR7735762;ERR7735783 2022KennettNatureCommunications I19170_ss I19170 0.016136994740014 0.0020213914537310002 0.8457168187217771 0.009038777630107001 +I19942_ss_MNT F Saki_Tzul n/a n/a n/a ST.18.11.8 Belize BZ Bladen Nature Reserve Saki Tzul 16.49 88.91 C14 PSUAMS-5896 4390 20 n/a C1c n/a bone_petrous 2 I19942.1240k;I19942.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 86156 0.3976838299505098 0.154777 3.353719e-15 ANGSD[v0.935] Nr Snps (per library): 147;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293362;ERR7735768;ERR7735789 2022KennettNatureCommunications I19942_ss I19942 0.010989461693872 0.0007275264807440001 0.772855490928931 0.0023005656022540002 +I19944_ss_MNT M Saki_Tzul n/a n/a n/a ST.18.11.9 Belize BZ Bladen Nature Reserve Saki Tzul 16.49 88.91 C14 PSUAMS-5879 4300 30 n/a C1c Q1a2a bone_petrous 2 I19944.1240k;I19944.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 47685 0.4192054760422649 n/a n/a n/a Nr Snps (per library): 12;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293364;ERR7735770;ERR7735791 2022KennettNatureCommunications I19944_ss I19944 0.010047336292098 0.012348639603561001 0.37281265254226204 0.372184100087229 +I19950_ss_MNT M Saki_Tzul n/a n/a n/a ST.17.7.14 Belize BZ Bladen Nature Reserve Saki Tzul 16.49 88.91 C14 PSUAMS-5172 4125 30 associated charcoal D4h3a5 Q1a2a1a1 bone_petrous 2 I19950.1240k;I19950.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 510230 0.2956663603885621 0.004544 6.312403e-15 ANGSD[v0.935] Nr Snps (per library): 2355;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293367;ERR7735773;ERR7735794 2022KennettNatureCommunications I19950_ss I19950 0.0023195152305030002 0.0034253594047150004 0.375118033775988 0.5381932347485301 +I20428_ss_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.14.1.a5 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-6381 6090 25 associated charcoal D n/a bone_petrous 2 I20428.1240k;I20428.mt OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 57537 0.44637616925274776 n/a n/a n/a Nr Snps (per library): 18;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293357;ERR7735763;ERR7735784 2022KennettNatureCommunications I20428_ss I20428 0.009689788079390001 0.01333129822432 0.39055876392820604 0.48736893750587607 +I24540_MNT F Mayahak_Cab_Pek n/a n/a n/a MHCP.19.12.18 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-7428 4875 25 associated charcoal C n/a bone_petrous 2 I24540.1240k;I24540.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 332108 0.25230876160923055 0.164347 5.615954e-14 ANGSD[v0.935] Nr Snps (per library): 1218;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293358;ERR7735764;ERR7735785 2022KennettNatureCommunications I24540 I24540 0.005941580798876 0.00071478558807 0.710631010852774 0.006966179240749001 +I24541_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.19.12.17 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-8121 10165 50 associated charcoal n/a n/a bone_petrous 2 I24541.1240k;I24541.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 2667 0.29096522700982635 n/a n/a n/a Nr Snps (per library): 0;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293353;ERR7735759;ERR7735780 2022KennettNatureCommunications I24541 I24541 0.05103733054937801 0.07883052490169301 0.291359378412651 0.45670544055538104 +I24542_MNT F Mayahak_Cab_Pek n/a n/a n/a MHCP.19.12.10 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-7434 4195 25 associated charcoal C1c n/a bone_petrous 2 I24542.mt;I24542.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 628663 0.21075627761597474 0.187255 6.388017e-13 ANGSD[v0.935] Nr Snps (per library): 0;4721. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293366;ERR7735793;ERR7735772 2022KennettNatureCommunications I24542 I24542 0.0033525615906750002 0.00036225406984000005 0.716734571954558 0.005669716740438001 +I3422_MNT U Unknown n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 I3442.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 0 0.149861878453039 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293361;ERR7735788 2022KennettNatureCommunications I3422 I3422 0.0 0.0 0.0 0.0 +I3442_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.14.1.5a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-1402 4415 25 n/a A2 Q1a2a1a1 bone_petrous 2 I3442.1240k;I3442_all.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 1031049 0.2596711248657115 0.012772 1.7661126500000004e-13 ANGSD[v0.935] Nr Snps (per library): 7185;9810. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293361;ERR7735767;ERR7735779 2022KennettNatureCommunications I3442 I3442 0.0009502020668760001 0.0013141380863180001 0.42617566134621204 0.537454481762157 +I5454_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.14.1.1 Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-2333 4430 20 n/a A2q Q1a2a1a1 bone_petrous 2 I5454.mt;I5454.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 653476 0.22011219213753763 0.006288 7.631344e-15 ANGSD[v0.935] Nr Snps (per library): 0;2338. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293360;ERR7735787;ERR7735766 2022KennettNatureCommunications I5454 I5454 0.002540898548954 0.0035255443742540004 0.399884165607206 0.507451889272863 +I5455_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.14.2.4a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 UCIAMS-186360 4005 20 n/a C1c Q1a2a1a1 bone_petrous 2 I5455.mt;I5455.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 770808 0.20799515504585195 0.010075 1.27581e-14 ANGSD[v0.935] Nr Snps (per library): 0;4163. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293370;ERR7735797;ERR7735776 2022KennettNatureCommunications I5455 I5455 0.001992944158201 0.0027840572516370002 0.40577041495764404 0.521870435557867 +I6235_MNT M Mayahak_Cab_Pek I6236_MNT second Described as second/third degree in publication. MHCP.14.1.2a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-1401 4050 30 n/a A2+(64)+@16111 Q1a2a1a1 bone_petrous 2 I6235.1240k;I6235.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 785721 0.19601622278892755 0.007254 5.081764e-14 ANGSD[v0.935] Nr Snps (per library): 4110;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293368;ERR7735774;ERR7735795 2022KennettNatureCommunications I6235 I6235 0.001776686130726 0.0024899820552310003 0.372952238486206 0.48262752397753206 +I6236_MNT F Saki_Tzul I6235_MNT second Described as second/third degree in publication. ST.16.1.1 Belize BZ Bladen Nature Reserve Saki Tzul 16.49 88.91 C14 PSUAMS-1403 4025 25 n/a C1c n/a bone_petrous 2 I6236.mt;I6236.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 852786 0.14737310993427039 0.248068 3.454863e-14 ANGSD[v0.935] Nr Snps (per library): 0;9169. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293369;ERR7735796;ERR7735775 2022KennettNatureCommunications I6236 I6236 0.002076795398914 0.00019118942399800001 0.7760150559139981 0.004467171704906001 +I7543_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.98.34.3a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4292 3565 20 n/a C1c n/a bone_petrous 1 I7543.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 0 0.362116991643454 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293372;ERR7735799 2022KennettNatureCommunications I7543 I7543 0.0 0.0 0.0 0.0 +I7543_ss_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.98.34.3a Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-4292 3565 20 enamel carbonate n/a n/a bone_petrous 1 I7543.1240k OtherCapture half ss haploid https://github.com/nf-core/eager/releases/tag/2.5.1 72433 0.36127843331408 n/a n/a n/a Nr Snps (per library): 37. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293372;ERR7735778 2022KennettNatureCommunications I7543_ss I7543 0.008786061456223 0.011759748503288 0.407408056358016 0.48158552250766506 +I7544_MNT F Mayahak_Cab_Pek n/a n/a n/a MHCP.98.34.4b Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 UCIAMS-228020 4210 20 n/a C1c n/a bone_petrous 2 I7544.mt;I7544.1240k OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 697178 0.22927157784035643 0.210122 1.167854e-12 ANGSD[v0.935] Nr Snps (per library): 0;5547. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293365;ERR7735792;ERR7735771 2022KennettNatureCommunications I7544 I7544 0.0035764932355230004 0.000352999728059 0.837917192158189 0.005558606650098 +I8041_MNT M Mayahak_Cab_Pek n/a n/a n/a MHCP.14.2.4c Belize BZ Bladen Nature Reserve Mayahak Cab Pek 16.49 88.91 C14 PSUAMS-2681 3735 20 n/a A2+(64)+@16111 Q1a2a1a1 bone_ulna 2 I8041.1240k;I8041.mt OtherCapture half ds haploid https://github.com/nf-core/eager/releases/tag/2.5.1 67870 0.17901956627724055 n/a n/a n/a Nr Snps (per library): 13;0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB49391;ERS9293371;ERR7735777;ERR7735798 2022KennettNatureCommunications I8041 I8041 0.012438095679637001 0.015162255735294 0.44910110137360404 0.44162587319616703 diff --git a/2022_Kennett_Belize/2022_Kennett_Belize.ssf b/2022_Kennett_Belize/2022_Kennett_Belize.ssf new file mode 100644 index 0000000..2f43d01 --- /dev/null +++ b/2022_Kennett_Belize/2022_Kennett_Belize.ssf @@ -0,0 +1,42 @@ +poseidon_IDs udg library_built sample_accession study_accession run_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp notes +I24541_MNT half ds SAMEA11646645 PRJEB49391 ERR7735759 I24541 ERS9293353 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24541.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735759/ERR7735759.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735759/ERR7735759.fastq.gz 1855984 b94d512e41912a947d15b4b24e3483cc 84417 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735759/I24541.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735759/I24541.1240k.bam.bai n/a +I19169_ss_MNT half ss SAMEA11646647 PRJEB49391 ERR7735761 I19169 ERS9293355 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19169.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735761/ERR7735761.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735761/ERR7735761.fastq.gz 92206050 6e7dd354c9c77956e490af0fb1f554e3 4025686 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735761/I19169.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735761/I19169.1240k.bam.bai n/a +I20428_ss_MNT half ss SAMEA11646649 PRJEB49391 ERR7735763 I20428 ERS9293357 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I20428.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735763/ERR7735763.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735763/ERR7735763.fastq.gz 57236928 1ca1027cb3fcba7418ff08472858cc2d 2354550 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735763/I20428.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735763/I20428.1240k.bam.bai n/a +I24540_MNT half ds SAMEA11646650 PRJEB49391 ERR7735764 I24540 ERS9293358 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24540.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735764/ERR7735764.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735764/ERR7735764.fastq.gz 95187043 da8dec8b26e3c861c413a14e53f9a1b1 3717844 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735764/I24540.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735764/I24540.1240k.bam.bai n/a +I3442_MNT half ds SAMEA11646653 PRJEB49391 ERR7735767 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735767/ERR7735767.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735767/ERR7735767.fastq.gz 498864434 8566ddacdd71bb872935254bf370d297 15675937 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735767/I3442.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735767/I3442.1240k.bam.bai n/a +I19942_ss_MNT half ss SAMEA11646654 PRJEB49391 ERR7735768 I19942 ERS9293362 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19942.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735768/ERR7735768.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735768/ERR7735768.fastq.gz 93890963 0925368e9095940e3af86fbcbf5cd94e 4131260 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735768/I19942.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735768/I19942.1240k.bam.bai n/a +I19944_ss_MNT half ss SAMEA11646656 PRJEB49391 ERR7735770 I19944 ERS9293364 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19944.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735770/ERR7735770.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735770/ERR7735770.fastq.gz 108012101 499cc8ea527239722020ba144ad2b90c 4740168 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735770/I19944.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735770/I19944.1240k.bam.bai n/a +I19950_ss_MNT half ss SAMEA11646659 PRJEB49391 ERR7735773 I19950 ERS9293367 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19950.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735773/ERR7735773.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735773/ERR7735773.fastq.gz 191943173 42e9cf1d1b386b77ef3ca8b0ceb6d6bf 6765002 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735773/I19950.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735773/I19950.1240k.bam.bai n/a +I3442_MNT half ds SAMEA11646653 PRJEB49391 ERR7735779 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442_all.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735779/ERR7735779.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735779/ERR7735779.fastq.gz 776592779 2bf8e4a23db81bae07c535c9e9e5cadc 24639708 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735779/I3442_all.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735779/I3442_all.1240k.bam.bai n/a +I19169_ss_MNT half ss SAMEA11646647 PRJEB49391 ERR7735782 I19169 ERS9293355 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19169.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735782/ERR7735782.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735782/ERR7735782.fastq.gz 72105 5bf37f58045d5831f779230731f0ebc4 3514 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735782/I19169.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735782/I19169.mt.bam.bai n/a +I20428_ss_MNT half ss SAMEA11646649 PRJEB49391 ERR7735784 I20428 ERS9293357 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I20428.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735784/ERR7735784.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735784/ERR7735784.fastq.gz 33445 a2f1105261d91e17ac4e976caa12e804 1393 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735784/I20428.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735784/I20428.mt.bam.bai n/a +I5454_MNT half ds SAMEA11646652 PRJEB49391 ERR7735787 I5454 ERS9293360 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5454.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735787/ERR7735787.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735787/ERR7735787.fastq.gz 521333 7b8ec25f512e7615989c98642c507a0c 24233 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735787/I5454.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735787/I5454.mt.bam.bai n/a +I19942_ss_MNT half ss SAMEA11646654 PRJEB49391 ERR7735789 I19942 ERS9293362 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19942.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735789/ERR7735789.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735789/ERR7735789.fastq.gz 201223 4fa2d37ae8078c52a53a62483cd7a5e2 11003 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735789/I19942.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735789/I19942.mt.bam.bai n/a +I19167_ss_MNT half ss SAMEA11646655 PRJEB49391 ERR7735790 I19167 ERS9293363 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19167.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735790/ERR7735790.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735790/ERR7735790.fastq.gz 28234 418e5ee553ed13d1d3c121801b1a8679 1180 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735790/I19167.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735790/I19167.mt.bam.bai n/a +I19944_ss_MNT half ss SAMEA11646656 PRJEB49391 ERR7735791 I19944 ERS9293364 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19944.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735791/ERR7735791.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735791/ERR7735791.fastq.gz 42701 a477939efc88ac3b22e704b4bbe849b6 1943 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735791/I19944.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735791/I19944.mt.bam.bai n/a +I24542_MNT half ds SAMEA11646658 PRJEB49391 ERR7735793 I24542 ERS9293366 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24542.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735793/ERR7735793.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735793/ERR7735793.fastq.gz 289822 0731e7a608ce9fd572670b198a68b677 16004 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735793/I24542.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735793/I24542.mt.bam.bai n/a +I5455_MNT half ds SAMEA11646662 PRJEB49391 ERR7735797 I5455 ERS9293370 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5455.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735797/ERR7735797.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735797/ERR7735797.fastq.gz 784884 f1c74a968f9b13207d2cce0a2762811b 35846 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735797/I5455.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735797/I5455.mt.bam.bai n/a +I8041_MNT half ds SAMEA11646663 PRJEB49391 ERR7735777 I8041 ERS9293371 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I8041.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/007/ERR7735777/ERR7735777.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/007/ERR7735777/ERR7735777.fastq.gz 18380223 2b8d1b8cc01480ade292e25db801cf0b 603701 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735777/I8041.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735777/I8041.1240k.bam.bai n/a +I24540_MNT half ds SAMEA11646650 PRJEB49391 ERR7735785 I24540 ERS9293358 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24540.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735785/ERR7735785.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735785/ERR7735785.fastq.gz 148274 ce23b18682cf1ec9e69832dd9e40c016 7854 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735785/I24540.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735785/I24540.mt.bam.bai n/a +I13267_MNT half ds SAMEA11646651 PRJEB49391 ERR7735786 I13267 ERS9293359 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13267.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735786/ERR7735786.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735786/ERR7735786.fastq.gz 1272330 ab15325f3cf4ab7b56617a7d2d262fbc 67580 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735786/I13267.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735786/I13267.mt.bam.bai n/a +I7544_MNT half ds SAMEA11646657 PRJEB49391 ERR7735792 I7544 ERS9293365 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7544.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735792/ERR7735792.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735792/ERR7735792.fastq.gz 648567 d14f517afbc4afbb683b2ff6970b8978 29401 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735792/I7544.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735792/I7544.mt.bam.bai n/a +I6236_MNT half ds SAMEA11646661 PRJEB49391 ERR7735796 I6236 ERS9293369 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6236.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735796/ERR7735796.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735796/ERR7735796.fastq.gz 795676 e002bcc601b5c9e688c8f9fcec2e3113 33015 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735796/I6236.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735796/I6236.mt.bam.bai n/a +I8041_MNT half ds SAMEA11646663 PRJEB49391 ERR7735798 I8041 ERS9293371 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I8041.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735798/ERR7735798.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735798/ERR7735798.fastq.gz 162249 d7d9439ea412afe12a06c12931c1c2ec 7073 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735798/I8041.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735798/I8041.mt.bam.bai n/a +I19170_ss_MNT half ss SAMEA11646648 PRJEB49391 ERR7735762 I19170 ERS9293356 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19170.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735762/ERR7735762.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735762/ERR7735762.fastq.gz 102399157 7073896ad40b7e7c4a447b0a55a3c817 4546278 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735762/I19170.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735762/I19170.1240k.bam.bai n/a +I19167_ss_MNT half ss SAMEA11646655 PRJEB49391 ERR7735769 I19167 ERS9293363 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19167.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735769/ERR7735769.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735769/ERR7735769.fastq.gz 24293929 30c12091d3f8fe7f78898b41d5018607 1033145 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735769/I19167.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735769/I19167.1240k.bam.bai n/a +I13268_MNT half ds SAMEA11646646 PRJEB49391 ERR7735781 I13268 ERS9293354 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13268.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735781/ERR7735781.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735781/ERR7735781.fastq.gz 115094 f87566e3c39293ac6026d6a255389f86 5869 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735781/I13268.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735781/I13268.mt.bam.bai n/a +I19170_ss_MNT half ss SAMEA11646648 PRJEB49391 ERR7735783 I19170 ERS9293356 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19170.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/003/ERR7735783/ERR7735783.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/003/ERR7735783/ERR7735783.fastq.gz 77913 3b04ff0592c6f3816f96bc2c0b01b3e3 3879 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735783/I19170.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735783/I19170.mt.bam.bai n/a +I3422_MNT half ds SAMEA11646653 PRJEB49391 ERR7735788 I3442 ERS9293361 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I3442.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735788/ERR7735788.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735788/ERR7735788.fastq.gz 501741 7e0e87abecf9b5efa09dbd55bd3156a6 23147 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735788/I3442.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735788/I3442.mt.bam.bai n/a +I5454_MNT half ds SAMEA11646652 PRJEB49391 ERR7735766 I5454 ERS9293360 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5454.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735766/ERR7735766.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735766/ERR7735766.fastq.gz 163253161 ea871baba48abc0f16d4511ae22d15b3 4944463 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735766/I5454.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735766/I5454.1240k.bam.bai n/a +I7544_MNT half ds SAMEA11646657 PRJEB49391 ERR7735771 I7544 ERS9293365 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7544.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/001/ERR7735771/ERR7735771.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/001/ERR7735771/ERR7735771.fastq.gz 367744844 245ea1075af45d30d3e5f6b5848aaf49 11753217 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735771/I7544.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735771/I7544.1240k.bam.bai n/a +I6235_MNT half ds SAMEA11646660 PRJEB49391 ERR7735774 I6235 ERS9293368 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6235.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735774/ERR7735774.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735774/ERR7735774.fastq.gz 287480585 3146050b10350356236efd02aabf085f 8818072 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735774/I6235.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735774/I6235.1240k.bam.bai n/a +I7543_ss_MNT half ss SAMEA11646664 PRJEB49391 ERR7735778 I7543 ERS9293372 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7543.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/008/ERR7735778/ERR7735778.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/008/ERR7735778/ERR7735778.fastq.gz 61592426 99fc43f8725e3beb25a4ae993171a502 2409685 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735778/I7543.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735778/I7543.1240k.bam.bai n/a +I19950_ss_MNT half ss SAMEA11646659 PRJEB49391 ERR7735794 I19950 ERS9293367 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I19950.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/004/ERR7735794/ERR7735794.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/004/ERR7735794/ERR7735794.fastq.gz 233670 6b569cbab201211164d110dfdd077ff4 11862 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735794/I19950.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735794/I19950.mt.bam.bai n/a +I6235_MNT half ds SAMEA11646660 PRJEB49391 ERR7735795 I6235 ERS9293368 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6235.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735795/ERR7735795.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735795/ERR7735795.fastq.gz 771971 2fdc7c35481530845dfa1934578cac47 34809 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735795/I6235.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735795/I6235.mt.bam.bai n/a +I7543_MNT half ds SAMEA11646664 PRJEB49391 ERR7735799 I7543 ERS9293372 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I7543.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/009/ERR7735799/ERR7735799.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/009/ERR7735799/ERR7735799.fastq.gz 93561 27738b9ec0e02f8fcf035e2ff27a6302 4295 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735799/I7543.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735799/I7543.mt.bam.bai n/a +I13268_ss_MNT half ss SAMEA11646646 PRJEB49391 ERR7735760 I13268 ERS9293354 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13268.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735760/ERR7735760.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735760/ERR7735760.fastq.gz 153779107 a9346a5a151ac8b06b80220d3a110b06 6415547 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735760/I13268.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735760/I13268.1240k.bam.bai n/a +I13267_MNT half ds SAMEA11646651 PRJEB49391 ERR7735765 I13267 ERS9293359 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I13267.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735765/ERR7735765.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735765/ERR7735765.fastq.gz 382102409 546573064bb13a22915b94886d1bc958 13317936 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735765/I13267.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735765/I13267.1240k.bam.bai n/a +I24542_MNT half ds SAMEA11646658 PRJEB49391 ERR7735772 I24542 ERS9293366 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24542.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/002/ERR7735772/ERR7735772.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/002/ERR7735772/ERR7735772.fastq.gz 290069082 c2c1ba335d30bd3ff43cb9272d782cf3 11630634 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735772/I24542.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735772/I24542.1240k.bam.bai n/a +I6236_MNT half ds SAMEA11646661 PRJEB49391 ERR7735775 I6236 ERS9293369 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I6236.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/005/ERR7735775/ERR7735775.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/005/ERR7735775/ERR7735775.fastq.gz 359469846 3f4edc6f41c196641e5a9be058069dab 10062021 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735775/I6236.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735775/I6236.1240k.bam.bai n/a +I5455_MNT half ds SAMEA11646662 PRJEB49391 ERR7735776 I5455 ERS9293370 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I5455.1240k OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/006/ERR7735776/ERR7735776.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/006/ERR7735776/ERR7735776.fastq.gz 237496024 791ad7c50b0a9e04aad6295de11b7ada 7141310 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735776/I5455.1240k.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735776/I5455.1240k.bam.bai n/a +I24541_MNT half ds SAMEA11646645 PRJEB49391 ERR7735780 I24541 ERS9293353 2022-02-07 2022-02-07 NextSeq 500 SINGLE GENOMIC ILLUMINA I24541.mt OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR773/000/ERR7735780/ERR7735780.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR773/000/ERR7735780/ERR7735780.fastq.gz 3084 f131746da555866f47a7b72033e5567f 101 ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735780/I24541.mt.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR773/ERR7735780/I24541.mt.bam.bai n/a diff --git a/2022_Kennett_Belize/CHANGELOG.md b/2022_Kennett_Belize/CHANGELOG.md new file mode 100644 index 0000000..2e440ea --- /dev/null +++ b/2022_Kennett_Belize/CHANGELOG.md @@ -0,0 +1,7 @@ +- V 1.0.0: Bump version for release +- V 0.3.0: Removed empty columns from janno +- V 0.2.2: Add bibFile and Publication info. +- V 0.2.1: Add janno info collected by @Kavlahkaff. Mirror info to fam file.Add @Kavlahkaff as Contributor. +- V 0.2.0: Rearrange Poseidon_IDs alphabetically. +- V 0.1.2: Automatic update of janno file from Minotaur processing. +- V 0.1.1: Added self as contributor to package. diff --git a/2022_Kennett_Belize/POSEIDON.yml b/2022_Kennett_Belize/POSEIDON.yml new file mode 100644 index 0000000..c6d5f24 --- /dev/null +++ b/2022_Kennett_Belize/POSEIDON.yml @@ -0,0 +1,28 @@ +poseidonVersion: 2.7.1 +title: 2022_Kennett_Belize +description: South-to-north migration preceded the advent of intensive farming in + the Maya region +contributor: +- name: Thiseas C. Lamnidis + email: thiseas_christos_lamnidis@eva.mpg.de +- name: Luca Thale-Bombien + email: luca_thale_bombien@eva.mpg.de +packageVersion: 1.0.0 +lastModified: 2024-12-20 +genotypeData: + format: PLINK + genoFile: 2022_Kennett_Belize.bed + genoFileChkSum: 88adc1ab1cb952796e4ea50e6f34cd9c + snpFile: 2022_Kennett_Belize.bim + snpFileChkSum: 433fa85a23f3123bade02348e4628b75 + indFile: 2022_Kennett_Belize.fam + indFileChkSum: cef50ec1c38fb84cde37d65e8a7cd57b + snpSet: 1240K +jannoFile: 2022_Kennett_Belize.janno +jannoFileChkSum: 8246f6325097954ebc31f128725508af +sequencingSourceFile: 2022_Kennett_Belize.ssf +sequencingSourceFileChkSum: 7c8e65c0edad90b85c84ce119d37f9ba +bibFile: 2022_Kennett_Belize.bib +bibFileChkSum: 17f919b194b2ae1d349af533fd870461 +readmeFile: README.md +changelogFile: CHANGELOG.md diff --git a/2022_Kennett_Belize/README.md b/2022_Kennett_Belize/README.md new file mode 100644 index 0000000..23b486f --- /dev/null +++ b/2022_Kennett_Belize/README.md @@ -0,0 +1,35 @@ +# 2022_Kennett_Belize +This package was created on 2024-11-26 and was processed using the following versions: + - nf-core/eager version: 2.5.1 + - Minotaur config version: 0.4.0dev + - CaptureType profile: 1240K + - CaptureType config version: 0.2.2dev + - Config template version: 0.3.0dev + - Package config version: 0.3.0dev + - Minotaur-packager version: 0.4.2dev + - populate_janno.py version: 0.4.1dev + +## Mirror Group_Name and Genetic_Sex from janno to fam +```bash +package_name="2022_Kennett_Belize" +paste -d "\t" ${package_name}/${package_name}.fam <(cut -f 1-3 ${package_name}/${package_name}.janno |tail -n +2) | \ + awk ' + BEGIN{ + OFS=IFS="\t" + } + { + $1=$9 + if ($8 == "M") { + $5=1 + } else if ($8 == "F") { + $5=2 + } + print $1,$2,$3,$4,$5,$6 + } + ' > tmp.fam +## Cannot overwrite in the same command that reads in the file, so an extra mv is needed. +mv tmp.fam ${package_name}/${package_name}.fam + +## trident version: 1.5.4.0 +trident rectify --packageVersion Patch --logText "Add janno info collected by @Kavlahkaff. Mirror info to fam file.Add @Kavlahkaff as Contributor." --checksumAll -d ${package_name} +``` \ No newline at end of file