TB-Profiler result

Run: SRR21277763
Summary

Run ID: SRR21277763

Sample name:

Date: 04-04-2023 01:40:30

Number of reads: 14299873

Percentage reads mapped: 97.7

Strain: lineage2.2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
embB 4247867 p.Val452Leu missense_variant 0.2 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490691 c.-92G>T upstream_gene_variant 0.1
fgd1 491309 p.Ala176Asp missense_variant 0.17
fgd1 491319 c.537G>A synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575499 p.Ala51Val missense_variant 0.33
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576175 c.828G>T synonymous_variant 0.15
mshA 576433 c.1086C>A synonymous_variant 0.11
mshA 576760 c.1413C>T synonymous_variant 0.11
ccsA 620264 p.Gly125Val missense_variant 0.11
ccsA 620272 p.Val128Met missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoB 761650 p.Ser615Asn missense_variant 0.1
rpoB 761686 p.Arg627Leu missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763912 c.543G>A synonymous_variant 0.11
rpoC 764547 p.Gly393Glu missense_variant 0.16
rpoC 764560 c.1191T>C synonymous_variant 0.29
rpoC 765289 c.1920G>A synonymous_variant 0.12
rpoC 766055 p.Gly896Cys missense_variant 0.95
rpoC 766993 p.Met1208Ile missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777283 c.1198C>T synonymous_variant 0.31
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801266 p.Gly153Val missense_variant 0.11
fbiC 1303135 p.Gly69Cys missense_variant 0.1
fbiC 1304426 p.Leu499Gln missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406953 p.Glu130* stop_gained 0.11
Rv1258c 1407098 c.243G>A synonymous_variant 0.5
Rv1258c 1407217 p.Gly42Arg missense_variant 0.11
embR 1417222 c.126G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674820 p.Leu207Ile missense_variant 0.11
inhA 1674826 p.Glu209* stop_gained 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834865 p.Gly442Arg missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918302 c.363G>T synonymous_variant 0.11
tlyA 1918566 c.627C>A synonymous_variant 0.12
tlyA 1918567 p.Ala210Thr missense_variant 0.11
tlyA 1918573 p.Ala212Thr missense_variant 0.14
tlyA 1918588 p.Glu217* stop_gained 0.17
tlyA 1918599 p.Trp220Cys missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170106 c.507C>A synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518583 p.Gln157Lys missense_variant 0.12
kasA 2518597 c.483C>A synonymous_variant 0.11
kasA 2518732 c.618C>T synonymous_variant 0.12
kasA 2519170 c.1056G>T synonymous_variant 0.17
kasA 2519174 p.Glu354* stop_gained 0.18
eis 2714858 p.Gly159Ser missense_variant 0.17
folC 2746298 p.Glu434Val missense_variant 0.12
folC 2746338 p.Ala421Thr missense_variant 0.25
folC 2746581 p.Glu340* stop_gained 0.11
folC 2747131 c.468C>A synonymous_variant 0.1
pepQ 2859603 c.816G>T synonymous_variant 0.12
pepQ 2859616 p.Ala268Asp missense_variant 0.1
pepQ 2859923 p.Gly166Cys missense_variant 0.2
pepQ 2859957 c.462G>A synonymous_variant 0.13
pepQ 2860143 c.276G>T synonymous_variant 0.11
pepQ 2860589 c.-171G>T upstream_gene_variant 0.67
ribD 2987301 c.463C>A synonymous_variant 0.11
ribD 2987306 c.468C>A synonymous_variant 0.18
ribD 2987377 p.Ser180Phe missense_variant 0.1
Rv2752c 3066286 c.-95C>T upstream_gene_variant 0.11
Rv2752c 3066299 c.-108C>A upstream_gene_variant 0.14
Rv2752c 3067017 c.-826G>T upstream_gene_variant 0.11
thyX 3067547 c.399C>A synonymous_variant 0.12
thyA 3074523 c.-52G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339034 c.-84G>T upstream_gene_variant 0.12
fbiD 3339051 c.-67C>T upstream_gene_variant 0.14
fbiD 3339324 c.207G>A synonymous_variant 0.1
fbiD 3339328 p.Ala71Thr missense_variant 0.13
fbiD 3339339 c.222G>T synonymous_variant 0.11
fbiD 3339346 p.Ala77Ser missense_variant 0.11
fbiD 3339555 c.438C>A synonymous_variant 0.16
fbiD 3339761 c.644G>T stop_lost&splice_region_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474928 p.Gly308Ser missense_variant 0.23
fprA 3474993 c.987G>T synonymous_variant 0.12
fprA 3475298 p.Arg431Gln missense_variant 0.12
fprA 3475303 p.Ala433Thr missense_variant 0.15
fprA 3475328 p.Arg441Leu missense_variant 0.15
fprA 3475354 p.Leu450Met missense_variant 0.12
Rv3236c 3612171 p.Glu316* stop_gained 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641638 p.Ala35Glu missense_variant 0.11
fbiB 3642391 p.Ala286Val missense_variant 0.11
fbiB 3642394 p.Pro287Leu missense_variant 0.12
fbiB 3642698 c.1164G>A synonymous_variant 0.14
alr 3841000 c.421C>T synonymous_variant 0.29
rpoA 3878592 c.-85C>A upstream_gene_variant 0.12
clpC1 4038182 c.2523C>T synonymous_variant 0.13
clpC1 4038211 p.Leu832Met missense_variant 0.11
clpC1 4040231 c.474C>T synonymous_variant 0.12
panD 4044479 c.-198C>T upstream_gene_variant 0.14
embC 4240999 p.Trp379* stop_gained 0.1
embC 4241008 c.1146G>T synonymous_variant 0.12
embC 4241143 c.1281C>T synonymous_variant 1.0
embC 4241246 p.Arg462Trp missense_variant 0.11
embC 4242366 p.Ser835Tyr missense_variant 0.12
embC 4242369 p.Arg836His missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243632 p.Gly134* stop_gained 0.14
embA 4243850 c.618G>A synonymous_variant 0.12
embA 4243971 p.Gly247* stop_gained 0.13
embA 4244212 p.Pro327His missense_variant 0.1
embA 4244550 p.Ala440Ser missense_variant 0.67
embA 4244848 p.Gly539Asp missense_variant 0.11
embA 4244915 c.1683G>T synonymous_variant 0.15
embB 4246646 p.Pro45Thr missense_variant 0.13
embB 4246797 p.Gly95Val missense_variant 0.2
embB 4246801 c.288G>T synonymous_variant 0.11
embB 4247014 c.501G>A synonymous_variant 0.12
embB 4247024 p.Pro171Thr missense_variant 0.22
embB 4247116 c.603G>T synonymous_variant 0.33
embB 4247264 p.Leu251Ile missense_variant 0.12
embB 4247631 p.Leu373His missense_variant 0.13
embB 4247802 p.Pro430Gln missense_variant 0.12
embB 4247805 p.Ala431Glu missense_variant 0.19
embB 4248599 p.Gly696Trp missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268276 c.561G>T synonymous_variant 0.12
aftB 4268886 c.-50G>T upstream_gene_variant 0.11
aftB 4268888 c.-52C>A upstream_gene_variant 0.14
ubiA 4269725 p.Leu37Met missense_variant 0.12
ethR 4327601 p.Ala18Glu missense_variant 0.11
whiB6 4338326 p.Ala66Thr missense_variant 0.13
whiB6 4338575 c.-54A>G upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0