TB-Profiler result

Run: ERR4831724
Summary

Run ID: ERR4831724

Sample name:

Date: 01-04-2023 21:05:02

Number of reads: 677725

Percentage reads mapped: 95.26

Strain: lineage2.2

Drug-resistance: HR-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 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 0.67 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 5111 c.-129C>A upstream_gene_variant 0.14
gyrB 5855 p.Ile206Leu missense_variant 0.11
gyrA 6517 c.-785G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7707 p.Pro136Ala missense_variant 0.12
gyrA 7856 p.Met185Ile missense_variant 0.15
gyrA 8602 p.Ala434Val missense_variant 0.17
gyrA 8731 p.Gly477Val missense_variant 0.25
gyrA 8871 p.Gly524Arg missense_variant 0.1
gyrA 9264 p.Asp655Tyr missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9380 p.Met693Ile missense_variant 0.17
gyrA 9395 c.2094G>T synonymous_variant 0.18
gyrA 9563 p.Met754Ile missense_variant 0.13
fgd1 490647 c.-136C>A upstream_gene_variant 0.29
fgd1 490856 p.Val25Ala missense_variant 0.29
fgd1 491661 c.879C>A synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619759 c.-132C>A upstream_gene_variant 0.33
ccsA 620368 p.Ala160Thr missense_variant 0.18
ccsA 620605 p.Val239Ile missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620805 c.915C>T synonymous_variant 0.15
rpoB 759850 p.Pro15Leu missense_variant 0.4
rpoB 760823 c.1017G>C synonymous_variant 0.25
rpoB 760833 p.His343Tyr missense_variant 0.17
rpoB 761129 c.1323G>T synonymous_variant 0.12
rpoB 761171 c.1365C>T synonymous_variant 0.22
rpoB 761178 p.Ser458Thr missense_variant 0.33
rpoB 761186 p.Glu460Asp missense_variant 0.22
rpoB 761189 c.1383T>C synonymous_variant 0.29
rpoB 761195 c.1389G>C synonymous_variant 0.33
rpoB 761198 c.1392G>C synonymous_variant 0.33
rpoB 761219 c.1413G>C synonymous_variant 0.25
rpoB 761234 c.1428G>C synonymous_variant 0.38
rpoB 761243 c.1437G>A synonymous_variant 0.25
rpoB 761345 c.1539G>A synonymous_variant 0.12
rpoB 761620 p.Met605Thr missense_variant 0.29
rpoB 761675 c.1869G>T synonymous_variant 0.4
rpoB 762500 p.Met898Ile missense_variant 0.22
rpoC 762959 c.-411G>C upstream_gene_variant 0.14
rpoC 762962 c.-408C>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763897 p.Lys176Asn missense_variant 0.2
rpoC 763972 c.603C>T synonymous_variant 0.25
rpoC 764143 c.774G>C synonymous_variant 0.17
rpoC 764147 p.Ser260Ala missense_variant 0.17
rpoC 764150 p.Ile261Val missense_variant 0.14
rpoC 764165 p.Glu266Gln missense_variant 0.14
rpoC 764746 c.1377G>T synonymous_variant 0.25
rpoC 764752 c.1383G>C synonymous_variant 0.29
rpoC 764758 c.1389C>G synonymous_variant 0.36
rpoC 764764 c.1395T>C synonymous_variant 0.36
rpoC 764791 c.1422C>G synonymous_variant 0.24
rpoC 764803 c.1434C>T synonymous_variant 0.24
rpoC 764809 c.1440C>T synonymous_variant 0.15
rpoC 764810 p.Pro481Ala missense_variant 0.17
rpoC 764815 c.1446A>G synonymous_variant 0.17
rpoC 764824 c.1455T>C synonymous_variant 0.17
rpoC 764827 c.1458G>C synonymous_variant 0.22
rpoC 764858 c.1489T>C synonymous_variant 0.12
rpoC 765370 c.2001G>C synonymous_variant 0.29
rpoC 765379 c.2010G>C synonymous_variant 0.22
rpoC 765382 c.2013G>T synonymous_variant 0.22
rpoC 765383 p.Met672Leu missense_variant 0.18
rpoC 765403 c.2034G>C synonymous_variant 0.2
rpoC 765405 p.Leu679His missense_variant 0.2
rpoC 765409 c.2040T>G synonymous_variant 0.17
rpoC 765421 c.2052C>G synonymous_variant 0.12
rpoC 765478 c.2109T>G synonymous_variant 0.11
rpoC 765654 p.Arg762His missense_variant 0.18
rpoC 765682 c.2313C>T synonymous_variant 0.15
rpoC 765702 p.Trp778Leu missense_variant 0.15
rpoC 766775 p.Arg1136Cys missense_variant 0.22
rpoC 766817 p.His1150Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776177 c.2304G>A synonymous_variant 0.25
mmpL5 776755 p.Asp576Asn missense_variant 0.14
mmpL5 777676 p.Leu269Met missense_variant 0.17
mmpL5 777746 c.735G>T synonymous_variant 0.5
mmpR5 778208 c.-782C>T upstream_gene_variant 0.33
mmpL5 778269 p.Ser71Leu missense_variant 0.25
mmpL5 778396 p.Arg29Gly missense_variant 0.17
mmpL5 779467 c.-987G>T upstream_gene_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781661 c.102C>T synonymous_variant 0.17
rplC 800777 c.-32C>T upstream_gene_variant 0.12
fbiC 1303480 p.Gln184Glu missense_variant 0.25
fbiC 1303710 p.Leu260Phe missense_variant 0.33
fbiC 1304799 c.1869G>T synonymous_variant 0.22
fbiC 1304946 c.2016G>A synonymous_variant 0.17
fbiC 1305168 c.2238C>T synonymous_variant 0.22
Rv1258c 1406293 p.Gly350Trp missense_variant 0.15
Rv1258c 1406356 p.Gln329* stop_gained 0.2
Rv1258c 1406732 c.609G>T synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
Rv1258c 1407488 c.-148C>A upstream_gene_variant 0.22
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.2
embR 1416232 p.Cys372Gly missense_variant 0.1
embR 1416591 p.Arg253Trp missense_variant 0.2
embR 1416643 c.705G>A synonymous_variant 0.22
embR 1416739 c.609C>T synonymous_variant 0.2
embR 1416824 p.Thr175Ile missense_variant 0.11
embR 1417127 p.Ser74Tyr missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.2
rrs 1472534 n.689G>T non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrl 1473860 n.203C>A non_coding_transcript_exon_variant 0.33
rrl 1474031 n.374T>C non_coding_transcript_exon_variant 0.5
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.5
rrl 1474591 n.934G>C non_coding_transcript_exon_variant 0.5
rrl 1475950 n.2293C>T non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.5
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.25
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.2
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.2
fabG1 1674108 p.Phe223Leu missense_variant 0.25
fabG1 1674176 p.Gly246Ala missense_variant 0.11
inhA 1674281 p.Arg27Pro missense_variant 0.14
rpsA 1833463 c.-79C>T upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834258 p.Glu239Asp missense_variant 0.17
rpsA 1834291 p.Glu250Asp missense_variant 0.13
rpsA 1834322 p.Glu261* stop_gained 0.13
rpsA 1834367 p.Leu276Phe missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918074 c.135C>T synonymous_variant 0.33
ndh 2101711 c.1332G>A synonymous_variant 0.15
ndh 2101889 p.Val385Ala missense_variant 0.25
ndh 2101965 p.Glu360Lys missense_variant 0.17
ndh 2102857 p.Ile62Met missense_variant 0.12
katG 2153994 c.2118G>A synonymous_variant 0.18
katG 2154491 p.Ala541Ser missense_variant 0.14
katG 2154673 p.Ala480Glu missense_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154929 p.Arg395Ser missense_variant 0.13
katG 2155168 p.Ser315Ala missense_variant 0.12
katG 2155877 p.Asp79Tyr missense_variant 0.2
katG 2156268 c.-157G>A upstream_gene_variant 0.17
katG 2156362 c.-251C>T upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168075 c.2538G>A synonymous_variant 0.22
PPE35 2168224 p.Pro797Ser missense_variant 0.14
PPE35 2170331 c.282G>A synonymous_variant 0.13
PPE35 2170453 p.Gly54Ser missense_variant 0.33
Rv1979c 2222820 c.345G>T synonymous_variant 0.12
Rv1979c 2223271 c.-107G>A upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288806 p.Ala146Ser missense_variant 0.12
pncA 2289446 c.-205G>A upstream_gene_variant 0.14
pncA 2289909 c.-668G>A upstream_gene_variant 0.14
pncA 2289977 c.-736C>A upstream_gene_variant 0.12
pncA 2289992 c.-751G>C upstream_gene_variant 0.12
eis 2714224 p.Ala370Val missense_variant 0.15
eis 2714344 p.Ala330Val missense_variant 0.17
eis 2714357 p.Gly326Ser missense_variant 0.12
eis 2714420 p.Leu305Ile missense_variant 0.25
eis 2714636 p.Leu233Ile missense_variant 0.13
eis 2715330 c.3G>A synonymous_variant 0.17
eis 2715519 c.-187G>C upstream_gene_variant 0.2
folC 2746411 c.1188G>A synonymous_variant 0.2
folC 2746469 p.Gly377Val missense_variant 0.22
folC 2746593 p.Pro336Ser missense_variant 0.17
folC 2746893 p.Arg236Cys missense_variant 0.25
folC 2747287 c.312G>A synonymous_variant 0.22
folC 2747395 c.204T>C synonymous_variant 0.33
pepQ 2859479 p.Gly314Ser missense_variant 0.33
pepQ 2860072 p.Gly116Asp missense_variant 0.18
pepQ 2860130 p.Phe97Ile missense_variant 0.13
pepQ 2860226 p.Ala65Ser missense_variant 0.33
pepQ 2860524 c.-106A>T upstream_gene_variant 0.13
ribD 2987144 p.Gln102His missense_variant 0.4
ribD 2987256 p.Pro140Ser missense_variant 0.18
Rv2752c 3064708 p.Arg495Pro missense_variant 0.2
Rv2752c 3065129 c.1063C>T synonymous_variant 1.0
Rv2752c 3065192 p.Ile334Val missense_variant 0.13
Rv2752c 3065537 p.Gly219Ser missense_variant 0.17
Rv2752c 3065573 p.Glu207Gln missense_variant 0.17
Rv2752c 3066361 c.-170G>C upstream_gene_variant 0.25
Rv2752c 3067037 c.-846G>T upstream_gene_variant 0.5
thyX 3067640 c.306G>A synonymous_variant 0.14
thyX 3067852 p.Gly32Arg missense_variant 0.29
thyX 3068074 c.-129C>G upstream_gene_variant 0.17
thyA 3073704 c.768G>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086821 c.6_7dupCG frameshift_variant 0.17
ald 3086880 p.Ala21Ser missense_variant 0.12
ald 3087066 p.Gly83Cys missense_variant 0.25
ald 3087322 p.Pro168Leu missense_variant 0.5
ald 3087377 c.558C>T synonymous_variant 0.25
ald 3087782 c.963G>A synonymous_variant 0.13
ald 3087812 c.993G>A synonymous_variant 0.18
ald 3087930 p.Ala371Thr missense_variant 0.25
fbiD 3339250 p.Asp45Tyr missense_variant 0.15
Rv3083 3449144 p.Pro214Gln missense_variant 0.17
Rv3083 3449278 p.Arg259Trp missense_variant 0.4
fprA 3473932 c.-75G>A upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474467 p.Gly154Asp missense_variant 0.12
fprA 3474810 c.804G>T synonymous_variant 0.17
fprA 3475166 p.Gly387Asp missense_variant 0.15
whiB7 3568500 c.180T>C synonymous_variant 0.2
whiB7 3568782 c.-103G>T upstream_gene_variant 0.13
Rv3236c 3612037 p.Phe360Leu missense_variant 0.78
Rv3236c 3612379 c.738G>C synonymous_variant 0.25
Rv3236c 3612398 p.Ala240Val missense_variant 0.5
Rv3236c 3612784 p.Leu111Phe missense_variant 0.33
Rv3236c 3612809 p.Pro103Leu missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613046 p.Val24Glu missense_variant 0.25
fbiA 3640488 c.-55G>T upstream_gene_variant 0.2
fbiA 3640800 p.Trp86Cys missense_variant 0.25
fbiB 3641838 p.Val102Ile missense_variant 0.12
fbiB 3642678 p.Gln382Lys missense_variant 0.33
alr 3840941 c.480C>T synonymous_variant 0.18
alr 3841241 p.Gln60His missense_variant 0.13
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3877502 p.Tyr336His missense_variant 0.2
rpoA 3877542 c.966C>A synonymous_variant 0.25
rpoA 3877545 c.963G>T synonymous_variant 0.25
rpoA 3877554 c.954G>A synonymous_variant 0.22
rpoA 3877560 c.948C>T synonymous_variant 0.29
rpoA 3877563 c.945C>T synonymous_variant 0.29
rpoA 3877569 p.Pro313Thr missense_variant 0.29
rpoA 3877587 c.921A>G synonymous_variant 0.22
rpoA 3877593 c.915C>T synonymous_variant 0.36
rpoA 3877614 c.894G>A synonymous_variant 0.17
rpoA 3877620 c.888G>A synonymous_variant 0.17
rpoA 3877638 c.870T>C synonymous_variant 0.2
rpoA 3877656 c.852T>G synonymous_variant 0.29
rpoA 3877677 c.831G>C synonymous_variant 0.29
rpoA 3877680 c.828G>C synonymous_variant 0.33
rpoA 3877686 c.822A>G synonymous_variant 0.33
rpoA 3877692 c.816G>C synonymous_variant 0.33
rpoA 3877704 c.804G>T synonymous_variant 0.29
rpoA 3877728 c.780C>G synonymous_variant 0.15
rpoA 3877731 c.777G>C synonymous_variant 0.15
rpoA 3877734 c.774G>C synonymous_variant 0.15
rpoA 3877737 c.771G>C synonymous_variant 0.17
rpoA 3877743 c.765T>C synonymous_variant 0.12
rpoA 3877749 c.759C>T synonymous_variant 0.13
rpoA 3877752 p.Asp252Glu missense_variant 0.14
rpoA 3877755 c.753C>T synonymous_variant 0.13
rpoA 3877758 c.750G>C synonymous_variant 0.13
rpoA 3877764 c.744C>A synonymous_variant 0.17
rpoA 3877770 c.738A>G synonymous_variant 0.18
rpoA 3877773 c.735G>C synonymous_variant 0.15
rpoA 3877776 c.732T>C synonymous_variant 0.15
rpoA 3877782 c.726T>C synonymous_variant 0.15
rpoA 3877797 c.711G>A synonymous_variant 0.18
rpoA 3877815 c.693C>T synonymous_variant 0.2
rpoA 3877867 p.Thr214Lys missense_variant 0.12
rpoA 3878267 p.Lys81Glu missense_variant 0.15
ddn 3986687 c.-157C>A upstream_gene_variant 0.17
clpC1 4038383 c.2322G>T synonymous_variant 0.17
clpC1 4038498 p.Ser736Ile missense_variant 1.0
clpC1 4038602 c.2103G>T synonymous_variant 0.15
clpC1 4038754 p.Gln651* stop_gained 0.15
clpC1 4039242 p.Leu488Arg missense_variant 0.18
clpC1 4040480 c.225T>C synonymous_variant 0.14
clpC1 4040495 c.210C>T synonymous_variant 0.12
clpC1 4040705 c.-1G>A upstream_gene_variant 0.14
panD 4043882 p.Pro134Ser missense_variant 0.22
panD 4044443 c.-162G>T upstream_gene_variant 0.18
embC 4239665 c.-198G>A upstream_gene_variant 0.18
embC 4239696 c.-167C>T upstream_gene_variant 0.17
embC 4239852 c.-11G>T upstream_gene_variant 0.25
embC 4240139 p.Gly93Arg missense_variant 0.17
embC 4240217 p.Arg119Cys missense_variant 0.14
embC 4240265 p.Arg135Cys missense_variant 0.15
embC 4240342 c.480C>T synonymous_variant 0.14
embC 4240569 p.Leu236Arg missense_variant 0.33
embC 4240756 c.894G>C synonymous_variant 0.12
embC 4240771 c.909G>C synonymous_variant 0.14
embC 4240772 p.Ser304Ala missense_variant 0.14
embC 4240778 p.His306Gly missense_variant 0.14
embC 4240781 p.Ala307Ser missense_variant 0.15
embC 4240789 c.927T>C synonymous_variant 0.13
embC 4240871 p.Val337Phe missense_variant 0.13
embC 4241524 c.1662G>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242836 p.Pro992Thr missense_variant 0.2
embA 4243348 p.Thr39Ile missense_variant 1.0
embA 4243471 p.Ala80Val missense_variant 1.0
embA 4244018 p.Leu262Phe missense_variant 0.15
embA 4244479 p.Thr416Met missense_variant 0.4
embA 4244781 p.Arg517Cys missense_variant 0.13
embA 4245071 c.1839G>C synonymous_variant 0.11
embA 4245083 c.1851A>C synonymous_variant 0.18
embA 4245089 c.1857G>C synonymous_variant 0.17
embA 4245092 c.1860C>G synonymous_variant 0.19
embA 4245094 p.Ile621Thr missense_variant 0.19
embA 4245101 c.1869G>C synonymous_variant 0.19
embA 4245125 c.1893G>C synonymous_variant 0.23
embA 4245179 p.Met649Ile missense_variant 0.13
embA 4245242 p.Tyr670* stop_gained 0.15
embA 4245444 p.Asp738Asn missense_variant 0.5
embA 4245661 p.Ala810Val missense_variant 0.22
embB 4245812 c.-702G>T upstream_gene_variant 0.22
embA 4246085 p.Glu951Asp missense_variant 0.17
embA 4246513 p.Pro1094Leu missense_variant 0.29
embB 4246774 c.261G>A synonymous_variant 0.2
embB 4246870 p.Ser119Arg missense_variant 0.22
embB 4246875 p.Gln121Arg missense_variant 0.22
embB 4247689 c.1176G>A synonymous_variant 0.29
embB 4249616 p.Gly1035Ser missense_variant 0.13
embB 4249688 p.Arg1059Ser missense_variant 0.14
aftB 4267380 p.Val486Glu missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268280 p.Arg186Gln missense_variant 0.15
ubiA 4269647 p.Ser63Arg missense_variant 0.25
ethA 4326676 p.Ser266Arg missense_variant 0.92
ethR 4326898 c.-651C>T upstream_gene_variant 0.25
ethA 4327179 p.Arg99Gly missense_variant 0.12
ethA 4328157 c.-684C>T upstream_gene_variant 0.18
whiB6 4338194 p.Arg110Trp missense_variant 0.25
whiB6 4338427 p.Gly32Val missense_variant 0.17
whiB6 4338582 c.-61G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407851 p.Arg118Cys missense_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408049 p.Cys52Arg missense_variant 0.11
gid 4408436 c.-234C>T upstream_gene_variant 0.17