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

Initial version of sars-cov-2 variant-reporting workflow #23

Merged
merged 7 commits into from
Mar 1, 2021
Merged

Initial version of sars-cov-2 variant-reporting workflow #23

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
2e8aca2
Initial version of srars-cov-2 variant-reporting workflow
mvdbeek Feb 22, 2021
fb65273
Install planemo version that outputs live logs
mvdbeek Feb 23, 2021
023703f
Make planemo verbose
mvdbeek Feb 24, 2021
1c4949e
Load both catWrapper tools
mvdbeek Feb 24, 2021
218f0be
Use cat1 1.0.0 which is available on 20.09 and 21.01
mvdbeek Feb 25, 2021
da32ab7
Updated workflow
mvdbeek Feb 26, 2021
05916ef
Fix input parameter workflow outputs
mvdbeek Feb 26, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .github/workflows/workflow_test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,7 @@ jobs:
mode: test
workflows: true
setup-cvmfs: true
planemo-version: 'https://github.com/mvdbeek/planemo/archive/load_both_cat_wrapper_distro_tools.zip'
repository-list: ${{ needs.setup.outputs.repository-list }}
galaxy-fork: ${{ env.GALAXY_FORK }}
galaxy-branch: ${{ env.GALAXY_BRANCH }}
Expand Down
7 changes: 7 additions & 0 deletions workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/.dockstore.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
version: 1.2
workflows:
- name: 'COVID-19-VARIATION-REPORTING'
primaryDescriptorPath: /variation-reporting.ga
subclass: Galaxy
testParameterFiles:
- /variation-reporting-test.yml
3 changes: 3 additions & 0 deletions workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
0.1
---------
- Initial version of COVID-19: variation analysis reporting
7 changes: 7 additions & 0 deletions workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
COVID-19: variation analysis reporting
--------------------------------------

This workflow takes table of variants produced by any of the other four variant
calling workflows in
https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling
and generates a list of variants by Samples and by Variant.
35 changes: 35 additions & 0 deletions ...sars-cov-2-variant-calling/sars-cov-2-variation-reporting/test-data/by_variant_report.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
POS REF ALT IMPACT FUNCLASS EFFECT GENE CODON AA TRID countunique(Sample) min(AF) max(AF) SAMPLES(above-thresholds) SAMPLES(all) AFs(all) change
174 G C . . . . . . . 2 0.863693 0.878632 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.878632,0.863693 G>C
241 C T . . . . . . . 4 0.045793 1 artic,illumina-wgs-se artic,illumina-wgs-se,illumina-wgs-pe,pe-artic 0.982659,1.0,0.049699,0.045793 C>T
490 T A MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gaT/gaA D75E leader 2 0.091743 0.09434 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.09434,0.091743 T>A
833 T C MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Ttc/Ctc F10L nsp2 1 0.888889 0.888889 artic artic 0.888889 T>C
1059 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCc/aTc T85I nsp2 1 0.959459 0.959459 artic artic 0.959459 C>T
1594 C T LOW SILENT SYNONYMOUS_CODING ORF1ab tcC/tcT S263 nsp2 2 0.866667 0.866667 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.866667,0.866667 C>T
2416 C T LOW SILENT SYNONYMOUS_CODING ORF1ab taC/taT Y537 nsp2 1 1 1 illumina-wgs-se illumina-wgs-se 1.0 C>T
3037 C T LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F106 nsp3 4 0.840708 1 artic,illumina-wgs-pe,illumina-wgs-se,pe-artic artic,illumina-wgs-se,illumina-wgs-pe,pe-artic 0.981651,1.0,0.842593,0.840708 C>T
3923 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Cct/Tct P402S nsp3 1 0.182927 0.182927 illumina-wgs-se illumina-wgs-se 0.182927 C>T
4523 G A MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Gct/Act A602T nsp3 1 1 1 illumina-wgs-se illumina-wgs-se 1.0 G>A
6285 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCc/aTc T1189I nsp3 2 0.615385 0.6875 pe-artic illumina-wgs-pe,pe-artic 0.615385,0.6875 C>T
6696 C CT HIGH NONE FRAME_SHIFT ORF1ab ctt/Tctt L1328S? nsp3 3 0.028169 0.160494 illumina-wgs-se illumina-wgs-se,illumina-wgs-pe,pe-artic 0.160494,0.028169,0.032051 C>CT
8290 C T LOW SILENT SYNONYMOUS_CODING ORF1ab ctC/ctT L1857 nsp3 2 0.84 0.844037 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.844037,0.84 C>T
10252 CT C HIGH NONE FRAME_SHIFT ORF1ab ttg/ L67 3Cpro 1 0.133333 0.133333 illumina-wgs-se illumina-wgs-se 0.133333 CT>C
10712 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Ctc/Ttc L220F 3Cpro 1 0.932584 0.932584 illumina-wgs-se illumina-wgs-se 0.932584 C>T
11109 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gCt/gTt A46V nsp6 2 0.896825 0.924528 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.924528,0.896825 C>T
13228 T G MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab ttT/ttG F68L nsp10 1 0.055336 0.055336 pe-artic pe-artic 0.055336 T>G
13660 A C LOW SILENT SYNONYMOUS_CODING ORF1ab Aga/Cga R74 RdRp 1 0.760383 0.760383 artic artic 0.760383 A>C
14408 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P323L RdRp 4 0.858407 1 artic,illumina-wgs-pe,illumina-wgs-se,pe-artic artic,illumina-wgs-se,illumina-wgs-pe,pe-artic 0.891156,1.0,0.873786,0.858407 C>T
15960 C T LOW SILENT SYNONYMOUS_CODING ORF1ab gcC/gcT A840 RdRp 2 0.11811 0.137681 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.11811,0.137681 C>T
16111 C T LOW SILENT SYNONYMOUS_CODING ORF1ab Cta/Tta L891 RdRp 1 0.897196 0.897196 illumina-wgs-se illumina-wgs-se 0.897196 C>T
17858 A G MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab tAt/tGt Y541C helicase 2 0.37931 0.392857 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.392857,0.37931 A>G
17874 C T LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F546 helicase 2 0.434783 0.458333 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.434783,0.458333 C>T
18788 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCa/aTa T250I ExoN 2 0.876812 0.877551 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.876812,0.877551 C>T
19684 G T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Gta/Tta V22L endoR 2 0.143713 0.143836 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.143836,0.143713 G>T
20209 AGTAGAAATT A MODERATE NONE CODON_CHANGE_PLUS_CODON_DELETION ORF1ab agtagaaattta/ata SRNL197I endoR 2 0.959746 0.972856 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.959746,0.972856 AGTAGAAATT>A
20897 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCa/cTa P80L MethTr 1 0.52 0.52 artic artic 0.52 C>T
20901 T C LOW SILENT SYNONYMOUS_CODING ORF1ab ggT/ggC G81 MethTr 1 0.469136 0.469136 artic artic 0.469136 T>C
23403 A G MODERATE MISSENSE NON_SYNONYMOUS_CODING S gAt/gGt D614G S 3 0.002573 1 artic,illumina-wgs-se artic,illumina-wgs-se,pe-artic 0.969231,1.0,0.002573 A>G
25208 AT A HIGH NONE FRAME_SHIFT S tgg/ W1217 S 1 0.104167 0.104167 illumina-wgs-se illumina-wgs-se 0.104167 AT>A
25563 G T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF3a caG/caT Q57H orf3a 4 0.847458 1 artic,illumina-wgs-pe,illumina-wgs-se,pe-artic artic,illumina-wgs-se,illumina-wgs-pe,pe-artic 0.965035,1.0,0.847458,0.850746 G>T
27964 C T MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF8 tCa/tTa S24L orf8 1 0.985507 0.985507 artic artic 0.985507 C>T
28253 C T LOW SILENT SYNONYMOUS_CODING ORF8 ttC/ttT F120 orf8 2 0.07767 0.088496 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.07767,0.088496 C>T
29700 A G . . . . . . . 2 0.101351 0.107914 illumina-wgs-pe,pe-artic illumina-wgs-pe,pe-artic 0.107914,0.101351 A>G
66 changes: 66 additions & 0 deletions ...ov-2-variant-calling/sars-cov-2-variation-reporting/test-data/combined_variant_report.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
Sample POS FILTER REF ALT DP AF SB DP4 IMPACT FUNCLASS EFFECT GENE CODON AA TRID min(AF) max(AF) countunique(change) countunique(FUNCLASS) change
artic 241 PASS C T 183 0.982659 0 0,0,82,88 . . . . . . . 0.045793 1 1 1 C>T
artic 833 PASS T C 151 0.888889 0 7,7,57,55 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Ttc/Ctc F10L nsp2 0.888889 0.888889 1 1 T>C
artic 1059 PASS C T 150 0.959459 0 2,2,71,71 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCc/aTc T85I nsp2 0.959459 0.959459 1 1 C>T
artic 3037 PASS C T 150 0.981651 0 1,0,55,52 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F106 nsp3 0.840708 1 1 1 C>T
artic 13660 PASS A C 319 0.760383 15 26,35,140,98 LOW SILENT SYNONYMOUS_CODING ORF1ab Aga/Cga R74 RdRp 0.760383 0.760383 1 1 A>C
artic 14408 PASS C T 153 0.891156 18 3,13,69,62 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P323L RdRp 0.858407 1 1 1 C>T
artic 20897 PASS C T 325 0.52 8 74,82,94,75 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCa/cTa P80L MethTr 0.52 0.52 1 1 C>T
artic 20901 PASS T C 325 0.469136 29 73,96,94,58 LOW SILENT SYNONYMOUS_CODING ORF1ab ggT/ggC G81 MethTr 0.469136 0.469136 1 1 T>C
artic 23403 PASS A G 147 0.969231 0 2,1,67,59 MODERATE MISSENSE NON_SYNONYMOUS_CODING S gAt/gGt D614G S 0.002573 1 1 1 A>G
artic 25563 PASS G T 148 0.965035 0 0,0,67,71 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF3a caG/caT Q57H orf3a 0.847458 1 1 1 G>T
artic 27964 PASS C T 146 0.985507 3 0,1,70,66 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF8 tCa/tTa S24L orf8 0.985507 0.985507 1 1 C>T
illumina-wgs-pe 174 PASS G C 585 0.878632 0 29,8,428,120 . . . . . . . 0.863693 0.878632 1 1 G>C
illumina-wgs-pe 241 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C T 664 0.049699 4 247,373,20,21 . . . . . . . 0.045793 1 1 1 C>T
illumina-wgs-pe 490 PASS T A 106 0.09434 0 61,35,6,4 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gaT/gaA D75E leader 0.091743 0.09434 1 1 T>A
illumina-wgs-pe 1594 PASS C T 15 0.866667 0 0,0,4,11 LOW SILENT SYNONYMOUS_CODING ORF1ab tcC/tcT S263 nsp2 0.866667 0.866667 1 1 C>T
illumina-wgs-pe 3037 PASS C T 108 0.842593 13 7,4,30,67 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F106 nsp3 0.840708 1 1 1 C>T
illumina-wgs-pe 6285 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C T 13 0.615385 0 4,1,6,2 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCc/aTc T1189I nsp3 0.615385 0.6875 1 1 C>T
illumina-wgs-pe 6696 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C CT 142 0.028169 0 43,98,1,3 HIGH NONE FRAME_SHIFT ORF1ab ctt/Tctt L1328S? nsp3 0.028169 0.160494 2 2 C>CT
illumina-wgs-pe 8290 PASS C T 109 0.844037 10 9,6,31,63 LOW SILENT SYNONYMOUS_CODING ORF1ab ctC/ctT L1857 nsp3 0.84 0.844037 1 1 C>T
illumina-wgs-pe 11109 PASS C T 106 0.924528 0 6,0,93,7 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gCt/gTt A46V nsp6 0.896825 0.924528 1 1 C>T
illumina-wgs-pe 14408 PASS C T 103 0.873786 1 3,5,48,47 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P323L RdRp 0.858407 1 1 1 C>T
illumina-wgs-pe 15960 PASS C T 127 0.11811 1 93,18,13,3 LOW SILENT SYNONYMOUS_CODING ORF1ab gcC/gcT A840 RdRp 0.11811 0.137681 1 1 C>T
illumina-wgs-pe 17858 PASS A G 28 0.392857 0 6,9,5,8 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab tAt/tGt Y541C helicase 0.37931 0.392857 1 1 A>G
illumina-wgs-pe 17874 PASS C T 23 0.434783 0 4,8,4,7 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F546 helicase 0.434783 0.458333 1 1 C>T
illumina-wgs-pe 18788 PASS C T 138 0.876812 0 6,6,58,67 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCa/aTa T250I ExoN 0.876812 0.877551 1 1 C>T
illumina-wgs-pe 19684 PASS G T 146 0.143836 0 105,19,19,3 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Gta/Tta V22L endoR 0.143713 0.143836 1 1 G>T
illumina-wgs-pe 20209 PASS AGTAGAAATT A 472 0.959746 21 12,7,398,55 MODERATE NONE CODON_CHANGE_PLUS_CODON_DELETION ORF1ab agtagaaattta/ata SRNL197I endoR 0.959746 0.972856 1 1 AGTAGAAATT>A
illumina-wgs-pe 25563 PASS G T 59 0.847458 0 0,5,4,50 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF3a caG/caT Q57H orf3a 0.847458 1 1 1 G>T
illumina-wgs-pe 28253 PASS C T 103 0.07767 0 67,26,7,3 LOW SILENT SYNONYMOUS_CODING ORF8 ttC/ttT F120 orf8 0.07767 0.088496 1 1 C>T
illumina-wgs-pe 29700 PASS A G 139 0.107914 0 45,78,5,10 . . . . . . . 0.101351 0.107914 1 1 A>G
illumina-wgs-se 241 PASS C T 81 1.0 0 0,0,38,43 . . . . . . . 0.045793 1 1 1 C>T
illumina-wgs-se 2416 PASS C T 65 1.0 0 0,0,34,31 LOW SILENT SYNONYMOUS_CODING ORF1ab taC/taT Y537 nsp2 1 1 1 1 C>T
illumina-wgs-se 3037 PASS C T 81 1.0 0 0,0,40,41 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F106 nsp3 0.840708 1 1 1 C>T
illumina-wgs-se 3923 PASS C T 82 0.182927 1 35,32,9,6 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Cct/Tct P402S nsp3 0.182927 0.182927 1 1 C>T
illumina-wgs-se 4523 PASS G A 80 1.0 0 0,0,43,37 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Gct/Act A602T nsp3 1 1 1 1 G>A
illumina-wgs-se 6696 PASS C CT 81 0.160494 0 35,34,7,6 HIGH NONE FRAME_SHIFT ORF1ab ctt/Tctt L1328S? nsp3 0.028169 0.160494 2 2 C>CT
illumina-wgs-se 6696 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C T 82 0.04878 0 40,38,2,2 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P1326L nsp3 0.028169 0.160494 2 2 C>T
illumina-wgs-se 10252 PASS CT C 75 0.133333 0 34,32,5,5 HIGH NONE FRAME_SHIFT ORF1ab ttg/ L67 3Cpro 0.133333 0.133333 1 1 CT>C
illumina-wgs-se 10712 PASS C T 89 0.932584 0 0,0,42,41 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Ctc/Ttc L220F 3Cpro 0.932584 0.932584 1 1 C>T
illumina-wgs-se 14408 PASS C T 94 1.0 0 0,0,47,47 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P323L RdRp 0.858407 1 1 1 C>T
illumina-wgs-se 16111 PASS C T 107 0.897196 0 5,6,47,49 LOW SILENT SYNONYMOUS_CODING ORF1ab Cta/Tta L891 RdRp 0.897196 0.897196 1 1 C>T
illumina-wgs-se 23403 PASS A G 105 1.0 0 0,0,54,51 MODERATE MISSENSE NON_SYNONYMOUS_CODING S gAt/gGt D614G S 0.002573 1 1 1 A>G
illumina-wgs-se 25208 PASS AT A 96 0.104167 1 44,42,6,4 HIGH NONE FRAME_SHIFT S tgg/ W1217 S 0.104167 0.104167 1 1 AT>A
illumina-wgs-se 25563 PASS G T 100 1.0 0 0,0,50,50 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF3a caG/caT Q57H orf3a 0.847458 1 1 1 G>T
pe-artic 174 PASS G C 807 0.863693 0 41,8,619,139 . . . . . . . 0.863693 0.878632 1 1 G>C
pe-artic 241 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C T 939 0.045793 4 338,543,25,30 . . . . . . . 0.045793 1 1 1 C>T
pe-artic 490 PASS T A 109 0.091743 1 64,35,6,4 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gaT/gaA D75E leader 0.091743 0.09434 1 1 T>A
pe-artic 1594 PASS C T 15 0.866667 0 0,0,4,11 LOW SILENT SYNONYMOUS_CODING ORF1ab tcC/tcT S263 nsp2 0.866667 0.866667 1 1 C>T
pe-artic 3037 PASS C T 113 0.840708 13 7,4,31,70 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F106 nsp3 0.840708 1 1 1 C>T
pe-artic 6285 PASS C T 16 0.6875 0 4,1,8,3 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCc/aTc T1189I nsp3 0.615385 0.6875 1 1 C>T
pe-artic 6696 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 C CT 156 0.032051 0 43,112,1,4 HIGH NONE FRAME_SHIFT ORF1ab ctt/Tctt L1328S? nsp3 0.028169 0.160494 2 2 C>CT
pe-artic 8290 PASS C T 125 0.84 9 9,9,32,75 LOW SILENT SYNONYMOUS_CODING ORF1ab ctC/ctT L1857 nsp3 0.84 0.844037 1 1 C>T
pe-artic 11109 PASS C T 126 0.896825 0 9,0,110,7 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab gCt/gTt A46V nsp6 0.896825 0.924528 1 1 C>T
pe-artic 13228 PASS T G 253 0.055336 27 82,154,0,16 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab ttT/ttG F68L nsp10 0.055336 0.055336 1 1 T>G
pe-artic 14408 PASS C T 113 0.858407 2 4,7,50,52 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab cCt/cTt P323L RdRp 0.858407 1 1 1 C>T
pe-artic 15960 PASS C T 138 0.137681 0 99,19,17,3 LOW SILENT SYNONYMOUS_CODING ORF1ab gcC/gcT A840 RdRp 0.11811 0.137681 1 1 C>T
pe-artic 17858 PASS A G 29 0.37931 0 6,9,5,8 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab tAt/tGt Y541C helicase 0.37931 0.392857 1 1 A>G
pe-artic 17874 PASS C T 24 0.458333 0 4,8,5,7 LOW SILENT SYNONYMOUS_CODING ORF1ab ttC/ttT F546 helicase 0.434783 0.458333 1 1 C>T
pe-artic 18788 PASS C T 147 0.877551 0 6,6,62,72 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab aCa/aTa T250I ExoN 0.876812 0.877551 1 1 C>T
pe-artic 19684 PASS G T 167 0.143713 0 123,19,22,3 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF1ab Gta/Tta V22L endoR 0.143713 0.143836 1 1 G>T
pe-artic 20209 PASS AGTAGAAATT A 921 0.972856 24 18,7,825,71 MODERATE NONE CODON_CHANGE_PLUS_CODON_DELETION ORF1ab agtagaaattta/ata SRNL197I endoR 0.959746 0.972856 1 1 AGTAGAAATT>A
pe-artic 23403 min_af_0.05Xmin_dp_1Xmin_dp_alt_10 A G 34976 0.002573 0 7392,27461,21,79 MODERATE MISSENSE NON_SYNONYMOUS_CODING S gAt/gGt D614G S 0.002573 1 1 1 A>G
pe-artic 25563 PASS G T 67 0.850746 0 0,6,4,57 MODERATE MISSENSE NON_SYNONYMOUS_CODING ORF3a caG/caT Q57H orf3a 0.847458 1 1 1 G>T
pe-artic 28253 PASS C T 113 0.088496 0 75,26,9,3 LOW SILENT SYNONYMOUS_CODING ORF8 ttC/ttT F120 orf8 0.07767 0.088496 1 1 C>T
pe-artic 29700 PASS A G 148 0.101351 0 45,85,6,11 . . . . . . . 0.101351 0.107914 1 1 A>G
Loading