TB-Profiler result

Run: ERR5866536

Summary

Run ID: ERR5866536

Sample name:

Date: 02-04-2023 00:45:07

Number of reads: 344412

Percentage reads mapped: 99.5

Strain: lineage2.2.1

Drug-resistance: MDR-TB


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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
lineage2.2 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
folC 2747151 p.Ser150Gly missense_variant 1.0 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala missense_variant 1.0 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
gyrB 5878 c.639G>T synonymous_variant 0.29
gyrB 6117 p.Trp293Leu missense_variant 0.15
gyrB 6160 c.921C>A synonymous_variant 0.22
gyrB 6785 p.Glu516* stop_gained 0.2
gyrA 7326 p.Asp9Tyr missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7400 p.Met33Ile missense_variant 0.38
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7685 c.384G>A synonymous_variant 0.2
gyrA 8549 c.1248C>A synonymous_variant 0.29
gyrA 8567 c.1266C>A synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490863 c.81C>A synonymous_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576304 c.957G>T synonymous_variant 0.33
mshA 576334 c.987G>T synonymous_variant 0.33
mshA 576701 p.Arg452Ser missense_variant 0.18
mshA 576709 c.1362C>A synonymous_variant 0.18
mshA 576736 c.1389G>T synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759824 p.Gln6His missense_variant 0.17
rpoB 760362 p.Asp186Tyr missense_variant 0.3
rpoB 760437 p.Asp211Tyr missense_variant 0.2
rpoB 760467 p.Asp221Tyr missense_variant 0.29
rpoB 760935 p.Glu377* stop_gained 0.4
rpoB 761011 c.1206_1207dupCG frameshift_variant 0.33
rpoB 761453 c.1647C>A synonymous_variant 0.2
rpoB 761790 p.Arg662Ser missense_variant 0.18
rpoB 762069 p.Asp755Tyr missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763071 p.Asp1089Tyr missense_variant 0.5
rpoB 763116 p.Glu1104* stop_gained 0.29
rpoC 763912 c.543G>T synonymous_variant 0.15
rpoC 764656 c.1287C>A synonymous_variant 0.22
rpoC 764677 c.1308C>A synonymous_variant 0.25
rpoC 764830 c.1461C>A synonymous_variant 0.25
rpoC 765461 p.Asn698His missense_variant 1.0
rpoC 766453 c.3088delC frameshift_variant 0.33
rpoC 766522 c.3153C>T synonymous_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766722 p.Pro1118Leu missense_variant 0.22
rpoC 766873 c.3504C>A synonymous_variant 0.22
rpoC 767200 p.Glu1277Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776216 c.2265G>T synonymous_variant 0.22
mmpL5 777124 p.Asp453Tyr missense_variant 0.21
mmpL5 778017 p.Gly155Val missense_variant 0.17
mmpL5 778055 p.Ser142Arg missense_variant 0.18
mmpL5 778137 p.Arg115Ile missense_variant 0.33
mmpL5 778260 p.Ser74* stop_gained 0.2
mmpR5 779085 p.Leu32Phe missense_variant 0.18
mmpR5 779449 p.Leu154Met missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303581 c.651G>T synonymous_variant 0.5
fbiC 1303809 p.Gln293His missense_variant 0.29
fbiC 1304163 c.1233G>T synonymous_variant 0.25
fbiC 1304907 c.1977C>A synonymous_variant 0.17
fbiC 1304970 c.2040G>T synonymous_variant 0.25
fbiC 1305203 p.Arg758Leu missense_variant 0.25
Rv1258c 1406156 c.1185C>A synonymous_variant 0.17
Rv1258c 1406241 p.Ala367Asp missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406846 c.495C>A synonymous_variant 0.21
Rv1258c 1407203 c.138C>A synonymous_variant 0.2
embR 1416272 p.Ser359Tyr missense_variant 0.23
embR 1416303 p.Gly349Cys missense_variant 0.15
embR 1417029 p.Asp107Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471717 n.-129G>T upstream_gene_variant 0.2
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.4
rrs 1473320 n.1475G>T non_coding_transcript_exon_variant 0.33
rrl 1474871 n.1214A>G non_coding_transcript_exon_variant 0.5
rrl 1476248 n.2591G>T non_coding_transcript_exon_variant 0.5
inhA 1674775 p.Gly192Cys missense_variant 0.33
rpsA 1833584 p.Asp15Tyr missense_variant 0.33
rpsA 1833648 p.Gly36Val missense_variant 0.18
rpsA 1833650 p.Asp37Tyr missense_variant 0.18
rpsA 1834019 p.Asp160Tyr missense_variant 0.2
rpsA 1834060 c.519C>A synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834181 p.Gly214Cys missense_variant 0.14
rpsA 1834210 c.669C>A synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917976 p.Arg13Trp missense_variant 0.18
tlyA 1917992 p.Arg18Leu missense_variant 0.2
tlyA 1918572 c.633C>A synonymous_variant 0.67
ndh 2102204 c.838delG frameshift_variant 0.12
ndh 2102561 p.Ser161Tyr missense_variant 0.21
katG 2154163 p.Ser650Tyr missense_variant 0.2
katG 2154511 p.Gly534Val missense_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155115 p.Leu333Ile missense_variant 0.29
katG 2155141 p.Thr324Asn missense_variant 0.25
katG 2155787 p.Ala109Thr missense_variant 1.0
katG 2156220 c.-109G>T upstream_gene_variant 0.33
katG 2156369 c.-258C>A upstream_gene_variant 0.33
PPE35 2167756 p.Phe953Leu missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168081 c.2532C>A synonymous_variant 0.2
PPE35 2168299 p.Pro772Thr missense_variant 0.25
PPE35 2168336 p.Leu759Phe missense_variant 0.29
PPE35 2168405 c.2208G>T synonymous_variant 0.29
PPE35 2168420 c.2193C>A synonymous_variant 0.29
PPE35 2168456 c.2157C>A synonymous_variant 0.4
PPE35 2170317 p.Ala99Asp missense_variant 0.2
Rv1979c 2221862 p.Arg435Ser missense_variant 0.25
Rv1979c 2222301 c.864C>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289211 c.22_30delGACGTGCAG conservative_inframe_deletion 1.0
pncA 2289281 c.-40G>A upstream_gene_variant 0.18
pncA 2289869 c.-628G>T upstream_gene_variant 0.18
kasA 2518064 c.-51G>T upstream_gene_variant 0.2
kasA 2518464 p.Gly117Asp missense_variant 0.33
kasA 2518546 p.Met144Ile missense_variant 0.33
kasA 2518815 p.Arg234His missense_variant 0.25
kasA 2518912 c.798G>T synonymous_variant 0.15
eis 2714337 p.Lys332Asn missense_variant 0.25
eis 2714428 p.Pro302Gln missense_variant 0.15
eis 2714699 p.Arg212Ser missense_variant 0.17
eis 2714970 c.363C>T synonymous_variant 0.22
eis 2715040 p.Arg98Leu missense_variant 0.29
eis 2715070 p.Ala88Glu missense_variant 0.33
folC 2746531 c.1068G>T synonymous_variant 0.29
folC 2746546 c.1053C>T synonymous_variant 0.29
folC 2746713 p.Glu296* stop_gained 0.33
pepQ 2859410 p.Arg337Ser missense_variant 0.17
pepQ 2859575 p.Ala282Ser missense_variant 0.29
pepQ 2859701 p.Gly240Cys missense_variant 0.2
pepQ 2860099 c.319delC frameshift_variant 0.29
pepQ 2860400 c.19C>A synonymous_variant 0.2
pepQ 2860416 c.3G>T synonymous_variant 0.44
pepQ 2860484 c.-66G>T upstream_gene_variant 0.22
ribD 2987433 p.Leu199Ile missense_variant 0.18
ribD 2987511 p.Arg225Ser missense_variant 0.18
ribD 2987527 p.Gly230Val missense_variant 0.25
Rv2752c 3064569 c.1623G>T synonymous_variant 0.33
Rv2752c 3065156 p.Glu346* stop_gained 0.18
Rv2752c 3065277 c.915C>A synonymous_variant 0.29
Rv2752c 3065315 p.Glu293* stop_gained 0.25
Rv2752c 3065651 p.Arg181Ser missense_variant 0.22
thyX 3067375 p.Ala191Ser missense_variant 0.2
thyA 3074527 c.-56C>A upstream_gene_variant 0.3
thyA 3074632 c.-161C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086993 c.174C>A synonymous_variant 0.25
ald 3087343 p.Gly175Val missense_variant 0.2
ald 3087390 p.Gly191Ser missense_variant 0.2
ald 3087398 c.579C>A synonymous_variant 0.2
ald 3087484 p.Ala222Val missense_variant 0.2
ald 3087560 c.741C>G synonymous_variant 0.18
fbiD 3338994 c.-124G>T upstream_gene_variant 0.18
fbiD 3339178 p.Ala21Ser missense_variant 0.18
fbiD 3339580 p.Gly155Cys missense_variant 0.2
fprA 3473890 c.-117C>A upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474031 p.Val9Leu missense_variant 0.22
fprA 3474579 c.573C>A synonymous_variant 0.25
fprA 3474730 p.Gly242Cys missense_variant 0.33
fprA 3475152 p.Leu382Phe missense_variant 0.29
fprA 3475195 p.Ser397Gly missense_variant 0.18
fprA 3475311 p.Glu435Asp missense_variant 0.15
fprA 3475320 c.1314G>T synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613022 p.Pro32Gln missense_variant 0.25
Rv3236c 3613025 p.Ser31* stop_gained 0.25
fbiB 3640581 c.-954C>A upstream_gene_variant 0.29
fbiA 3640867 p.Leu109Met missense_variant 0.18
fbiA 3640930 p.Glu130* stop_gained 0.33
fbiA 3641514 p.Cys324* stop_gained 0.4
fbiB 3641920 p.Ala129Asp missense_variant 0.29
fbiB 3642029 c.495C>A synonymous_variant 0.2
fbiB 3642042 p.Leu170Met missense_variant 0.22
alr 3840800 c.621C>A synonymous_variant 0.22
alr 3841611 c.-191G>T upstream_gene_variant 0.29
ddn 3986848 p.Pro2Gln missense_variant 0.25
clpC1 4039823 c.882T>C synonymous_variant 0.11
clpC1 4039979 c.726C>A synonymous_variant 0.25
clpC1 4040131 p.Gly192Cys missense_variant 0.33
clpC1 4040527 p.Arg60Ser missense_variant 0.25
clpC1 4040729 c.-25G>T upstream_gene_variant 0.25
clpC1 4040798 c.-94G>T upstream_gene_variant 0.18
panD 4044009 c.273G>T synonymous_variant 0.22
embC 4239735 c.-128C>A upstream_gene_variant 0.4
embC 4239764 c.-99G>T upstream_gene_variant 0.33
embC 4240304 p.Leu148Ile missense_variant 0.22
embC 4240349 c.487C>A synonymous_variant 0.2
embC 4241918 p.Asp686Tyr missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243258 p.Ser9Tyr missense_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243787 c.555G>A synonymous_variant 0.29
embA 4243838 c.606C>A synonymous_variant 0.2
embA 4243966 p.Arg245Leu missense_variant 0.15
embA 4243976 p.Phe248Leu missense_variant 0.23
embA 4244825 c.1593G>T synonymous_variant 0.18
embA 4245311 c.2079C>A synonymous_variant 0.18
embA 4245410 c.2178C>A synonymous_variant 0.4
embA 4246066 c.2837dupC frameshift_variant 0.29
embB 4247050 c.537C>A synonymous_variant 0.25
embB 4247269 c.756C>A synonymous_variant 0.18
embB 4247377 c.864G>T synonymous_variant 0.18
embB 4248289 p.Trp592Cys missense_variant 0.18
embB 4248305 c.1792C>T synonymous_variant 0.18
embB 4249705 c.3192G>T synonymous_variant 0.22
embB 4249739 p.Ala1076Ser missense_variant 0.22
embB 4249773 p.Gly1087Val missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267732 p.Arg369Ser missense_variant 0.25
aftB 4268113 p.Ala242Ser missense_variant 0.17
aftB 4268184 p.Gly218Val missense_variant 0.18
ubiA 4269854 c.-21G>T upstream_gene_variant 0.33
ethA 4326023 p.Pro484His missense_variant 0.15
ethA 4326974 p.Trp167Leu missense_variant 0.17
ethR 4327588 p.Gly14Cys missense_variant 0.15
ethR 4327663 p.Asp39Tyr missense_variant 0.17
ethR 4327693 p.Asp49Tyr missense_variant 0.18
ethA 4328287 c.-814G>T upstream_gene_variant 0.25
ethA 4328293 c.-820C>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338709 c.-188G>T upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0