TB-Profiler result

Run: ERR4821128
Summary

Run ID: ERR4821128

Sample name:

Date: 01-04-2023 17:04:41

Number of reads: 1038869

Percentage reads mapped: 94.47

Strain: lineage4.1.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;X;H None 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 0.13 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 5045 c.-195C>A upstream_gene_variant 0.2
gyrB 5069 c.-171G>T upstream_gene_variant 0.14
gyrB 5594 p.Gly119Arg missense_variant 0.18
gyrB 5695 p.Lys152Asn missense_variant 0.13
gyrB 6445 p.Asp402Glu missense_variant 0.14
gyrB 6635 p.Ser466Pro missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7414 p.Gly38Ala missense_variant 0.17
gyrA 7569 p.Ala90Thr missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7652 c.351C>A synonymous_variant 0.25
gyrA 8365 p.Thr355Met missense_variant 0.15
gyrA 8688 p.Ala463Ser missense_variant 0.22
gyrA 8849 c.1548C>G synonymous_variant 0.13
gyrA 8931 p.Val544Met missense_variant 0.13
gyrA 9134 c.1833C>A synonymous_variant 0.17
gyrA 9144 p.Arg615Cys missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
gyrA 9638 c.2337C>A synonymous_variant 0.14
gyrA 9658 p.Thr786Ile missense_variant 0.17
fgd1 490744 c.-39T>C upstream_gene_variant 0.14
fgd1 490745 c.-38G>A upstream_gene_variant 0.17
fgd1 490875 c.93C>T synonymous_variant 0.18
fgd1 491151 c.369G>C synonymous_variant 0.12
fgd1 491187 c.405G>T synonymous_variant 0.18
fgd1 491728 p.Asp316Asn missense_variant 0.17
mshA 575254 c.-94C>T upstream_gene_variant 0.25
mshA 575632 c.285G>A synonymous_variant 0.25
mshA 575661 p.Pro105His missense_variant 0.18
mshA 576013 p.Arg222Ser missense_variant 0.4
ccsA 620124 c.234G>T synonymous_variant 0.18
ccsA 620721 c.831G>A synonymous_variant 0.33
ccsA 620741 p.Thr284Lys missense_variant 0.29
rpoB 759657 c.-150G>T upstream_gene_variant 0.14
rpoB 759715 c.-91delA upstream_gene_variant 0.15
rpoB 759827 p.Ser7Arg missense_variant 0.2
rpoB 760499 c.693G>A synonymous_variant 0.14
rpoB 760626 p.Lys274Glu missense_variant 0.11
rpoB 760670 c.864G>T synonymous_variant 0.12
rpoB 761064 p.Ala420Thr missense_variant 0.25
rpoB 761166 p.Pro454Thr missense_variant 0.2
rpoB 761945 c.2139G>A synonymous_variant 0.14
rpoB 762176 c.2370T>C synonymous_variant 0.13
rpoB 762185 c.2379G>C synonymous_variant 0.12
rpoB 762663 p.Leu953Met missense_variant 0.2
rpoC 762989 c.-381G>T upstream_gene_variant 0.18
rpoB 763261 p.Ala1152Val missense_variant 0.14
rpoC 763373 p.Leu2Ile missense_variant 0.29
rpoC 763558 c.189C>T synonymous_variant 0.14
rpoC 763620 p.Arg84His missense_variant 0.18
rpoC 763971 p.Gly201Val missense_variant 0.33
rpoC 763997 p.Asp210Asn missense_variant 0.5
rpoC 764109 p.Arg247His missense_variant 0.13
rpoC 764384 p.Asp339Tyr missense_variant 0.17
rpoC 764395 p.Asp342Glu missense_variant 0.11
rpoC 764671 c.1302G>A synonymous_variant 0.17
rpoC 764781 p.Ser471Asn missense_variant 0.17
rpoC 764873 p.Pro502Ser missense_variant 0.13
rpoC 764979 p.Asp537Gly missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765282 p.Thr638Asn missense_variant 0.12
rpoC 766105 c.2736C>A synonymous_variant 0.18
rpoC 766229 p.Ala954Ser missense_variant 0.18
rpoC 766278 p.Thr970Asn missense_variant 0.13
rpoC 766625 p.Leu1086Met missense_variant 0.12
rpoC 766696 c.3327G>A synonymous_variant 0.25
rpoC 766780 p.Glu1137Asp missense_variant 0.25
rpoC 766799 p.Ala1144Ser missense_variant 0.14
rpoC 766984 c.3615G>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775947 p.Ala845Asp missense_variant 0.18
mmpL5 776103 p.Ile793Thr missense_variant 0.2
mmpL5 776203 p.Gly760Cys missense_variant 0.2
mmpL5 776448 p.Glu678Gly missense_variant 0.33
mmpL5 776758 p.Asp575Asn missense_variant 0.25
mmpL5 776870 c.1611G>A synonymous_variant 0.17
mmpL5 777598 p.Arg295Trp missense_variant 0.2
mmpL5 777611 c.870G>T synonymous_variant 0.17
mmpL5 777766 p.Gly239Trp missense_variant 0.25
mmpL5 778585 c.-105C>A upstream_gene_variant 0.4
mmpS5 778881 p.Trp9Arg missense_variant 0.14
mmpR5 779048 p.Val20Asp missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
rplC 801017 p.Tyr70Cys missense_variant 0.17
fbiC 1302830 c.-101T>C upstream_gene_variant 0.12
fbiC 1304219 p.Pro430Leu missense_variant 0.22
fbiC 1304392 p.Pro488Ser missense_variant 0.17
fbiC 1304610 c.1680C>T synonymous_variant 1.0
fbiC 1305016 p.Thr696Pro missense_variant 0.12
fbiC 1305021 c.2091C>A synonymous_variant 0.14
fbiC 1305132 c.2202C>T synonymous_variant 0.22
fbiC 1305153 c.2223G>A synonymous_variant 0.2
fbiC 1305234 c.2304G>A synonymous_variant 0.2
fbiC 1305395 p.Ser822Tyr missense_variant 0.18
Rv1258c 1406431 p.Val304Phe missense_variant 0.15
Rv1258c 1406532 p.Gly270Val missense_variant 0.12
Rv1258c 1406693 c.648G>T synonymous_variant 0.15
Rv1258c 1406754 p.Ala196Asp missense_variant 0.17
embR 1416310 c.1038G>A synonymous_variant 0.12
embR 1416376 p.Asn324Lys missense_variant 0.31
embR 1416526 c.822C>G synonymous_variant 0.12
embR 1416618 p.Gly244Ser missense_variant 0.17
embR 1416736 c.612G>T synonymous_variant 0.29
embR 1416792 c.555delG frameshift_variant 0.13
embR 1416981 p.Val123Met missense_variant 0.17
embR 1417062 p.Ala96Thr missense_variant 0.18
embR 1417522 c.-175C>A upstream_gene_variant 0.2
embR 1417544 c.-197T>A upstream_gene_variant 0.17
atpE 1461117 p.Gly25Cys missense_variant 0.15
atpE 1461152 c.108C>A synonymous_variant 0.25
rrs 1471657 n.-189G>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471673 n.-173C>T upstream_gene_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0
rrl 1473483 n.-175C>A upstream_gene_variant 0.33
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
fabG1 1674124 p.Ala229Ser missense_variant 0.5
fabG1 1674151 p.Pro238Thr missense_variant 0.13
inhA 1674391 p.Asp64Asn missense_variant 0.2
inhA 1674733 p.Glu178* stop_gained 0.14
rpsA 1833413 c.-129G>A upstream_gene_variant 0.2
rpsA 1833480 c.-62G>T upstream_gene_variant 0.17
rpsA 1833743 c.202C>T synonymous_variant 0.15
rpsA 1834395 p.Arg285Gln missense_variant 0.13
rpsA 1834399 c.858C>T synonymous_variant 0.13
rpsA 1834617 p.Ser359Leu missense_variant 0.14
rpsA 1834735 c.1194C>T synonymous_variant 0.2
rpsA 1834953 p.Ala471Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918025 p.Ala29Val missense_variant 0.25
tlyA 1918514 p.Val192Asp missense_variant 0.14
ndh 2101717 c.1326C>T synonymous_variant 0.18
ndh 2101747 c.1296C>T synonymous_variant 0.13
ndh 2102966 p.Gly26Val missense_variant 0.13
katG 2153894 p.Arg740Ser missense_variant 0.17
katG 2154077 p.Gln679Lys missense_variant 0.14
katG 2154161 p.Glu651* stop_gained 0.25
katG 2154324 p.Asn596Lys missense_variant 0.13
katG 2154707 p.Val469Ile missense_variant 0.12
katG 2154785 p.Pro443Thr missense_variant 0.13
katG 2154944 p.Tyr390Asn missense_variant 0.18
katG 2155493 p.Asp207Asn missense_variant 0.17
katG 2155674 c.438G>T synonymous_variant 0.5
katG 2155764 c.348C>T synonymous_variant 0.25
katG 2155797 p.Met105Ile missense_variant 0.25
katG 2155834 p.Ala93Asp missense_variant 0.18
katG 2156062 p.Ser17Ile missense_variant 0.18
katG 2156236 c.-125C>T upstream_gene_variant 0.17
katG 2156347 c.-236G>A upstream_gene_variant 0.2
katG 2156501 c.-390C>T upstream_gene_variant 0.25
katG 2156559 c.-448C>T upstream_gene_variant 0.25
PPE35 2167876 p.Gly913Ser missense_variant 0.18
PPE35 2167984 p.Gly877Cys missense_variant 0.18
PPE35 2168067 p.Phe849Ser missense_variant 0.2
PPE35 2168638 p.Pro659Thr missense_variant 0.2
PPE35 2169217 p.Glu466* stop_gained 0.17
PPE35 2170031 c.582C>G synonymous_variant 0.12
PPE35 2170096 p.Arg173Trp missense_variant 0.5
PPE35 2170513 c.100C>T synonymous_variant 0.15
PPE35 2170633 c.-21C>T upstream_gene_variant 0.17
Rv1979c 2221808 p.Val453Leu missense_variant 0.14
Rv1979c 2222030 p.Val379Met missense_variant 0.15
Rv1979c 2222095 p.Ala357Val missense_variant 0.29
Rv1979c 2222812 p.Leu118Ser missense_variant 0.22
Rv1979c 2222870 p.Ala99Thr missense_variant 0.25
Rv1979c 2223159 c.6C>T synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289145 p.Asp33Tyr missense_variant 0.25
pncA 2289169 p.Ala25Ser missense_variant 0.33
pncA 2289287 c.-46C>A upstream_gene_variant 0.2
pncA 2289318 c.-77G>T upstream_gene_variant 0.17
pncA 2289465 c.-224G>T upstream_gene_variant 0.14
pncA 2289543 c.-302G>C upstream_gene_variant 0.22
kasA 2518602 p.Gly163Val missense_variant 0.15
kasA 2518844 p.Ala244Ser missense_variant 0.25
kasA 2518882 c.768C>T synonymous_variant 0.18
kasA 2519002 p.Glu296Asp missense_variant 0.17
kasA 2519159 p.Ala349Ser missense_variant 0.18
kasA 2519201 p.Arg363Ser missense_variant 0.22
eis 2714219 p.Ala372Thr missense_variant 0.14
eis 2715008 p.Ala109Ser missense_variant 0.13
eis 2715327 c.6T>C synonymous_variant 0.12
ahpC 2725967 c.-226G>T upstream_gene_variant 0.12
ahpC 2726259 p.Leu23Val missense_variant 0.15
folC 2746471 c.1128C>A synonymous_variant 0.14
folC 2746579 c.1020G>A synonymous_variant 0.14
folC 2746590 p.Gly337Cys missense_variant 0.17
folC 2746885 c.714C>T synonymous_variant 0.17
folC 2747420 p.Pro60His missense_variant 0.15
folC 2747755 c.-157C>A upstream_gene_variant 0.2
pepQ 2859642 c.777C>T synonymous_variant 0.2
pepQ 2859680 p.Leu247Ile missense_variant 0.14
pepQ 2859883 p.Leu179Pro missense_variant 0.14
pepQ 2860470 c.-52G>A upstream_gene_variant 0.17
ribD 2987231 c.393G>A synonymous_variant 0.2
ribD 2987358 p.Asp174Tyr missense_variant 0.14
ribD 2987393 c.555C>T synonymous_variant 0.17
Rv2752c 3065353 p.Arg280Leu missense_variant 0.17
Rv2752c 3065647 p.Pro182Arg missense_variant 0.17
Rv2752c 3065942 p.Glu84* stop_gained 0.25
Rv2752c 3066035 p.Asp53Tyr missense_variant 0.14
thyX 3067346 c.600C>T synonymous_variant 0.18
thyX 3067401 p.Arg182His missense_variant 0.15
thyX 3067432 p.Arg172Ser missense_variant 0.17
thyX 3067542 p.Ala135Asp missense_variant 0.33
thyA 3074118 c.354G>A synonymous_variant 0.25
thyA 3074124 c.348G>A synonymous_variant 0.2
thyA 3074311 p.Ser54Leu missense_variant 0.14
thyA 3074373 p.Gln33His missense_variant 0.29
thyA 3074578 c.-107C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087165 p.Ala116Thr missense_variant 0.2
ald 3087600 p.Gly261Cys missense_variant 0.14
ald 3087719 c.900C>T synonymous_variant 0.15
fbiD 3339069 c.-49C>A upstream_gene_variant 0.15
fbiD 3339199 p.Pro28Ser missense_variant 0.4
fbiD 3339240 c.123C>T synonymous_variant 0.33
fbiD 3339255 c.138G>A synonymous_variant 0.2
fbiD 3339341 p.Leu75Gln missense_variant 0.17
Rv3083 3448867 p.His122Tyr missense_variant 0.14
Rv3083 3449030 p.Ser176Tyr missense_variant 0.17
fprA 3473809 c.-198G>A upstream_gene_variant 0.14
fprA 3473947 c.-60G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474051 c.45G>T synonymous_variant 0.29
fprA 3475052 p.Asn349Ser missense_variant 0.13
whiB7 3568578 c.102C>A synonymous_variant 0.2
whiB7 3568592 p.Ala30Thr missense_variant 0.17
Rv3236c 3612427 c.690G>A synonymous_variant 0.15
Rv3236c 3612680 p.Arg146Gln missense_variant 0.25
Rv3236c 3613061 p.Ala19Val missense_variant 0.33
fbiA 3640558 p.Leu6Met missense_variant 0.13
fbiA 3640639 p.Ala33Pro missense_variant 0.11
fbiB 3641112 c.-423T>C upstream_gene_variant 0.17
fbiB 3641687 p.Lys51Asn missense_variant 0.2
fbiB 3641709 p.Arg59Trp missense_variant 0.14
fbiB 3642257 p.Phe241Leu missense_variant 0.12
fbiB 3642657 p.Val375Ile missense_variant 0.29
fbiB 3642711 p.Leu393Met missense_variant 0.15
fbiB 3642722 c.1188C>T synonymous_variant 0.18
alr 3840252 p.Val390Ala missense_variant 0.11
alr 3841495 c.-75G>A upstream_gene_variant 0.17
alr 3841512 c.-92C>A upstream_gene_variant 0.17
alr 3841515 c.-95C>A upstream_gene_variant 0.17
alr 3841525 c.-105G>T upstream_gene_variant 0.17
rpoA 3877571 p.Pro313Ser missense_variant 0.2
rpoA 3877801 p.Pro236Leu missense_variant 0.2
rpoA 3877803 c.705G>T synonymous_variant 0.2
ddn 3986957 c.114C>T synonymous_variant 0.13
ddn 3987021 c.178C>A synonymous_variant 0.15
clpC1 4038225 p.Pro827Leu missense_variant 0.33
clpC1 4038676 p.Val677Phe missense_variant 0.12
clpC1 4039042 p.Ser555Thr missense_variant 0.2
clpC1 4039107 p.Arg533Leu missense_variant 0.15
clpC1 4039532 c.1173C>T synonymous_variant 0.14
clpC1 4040760 c.-56C>A upstream_gene_variant 0.14
panD 4044114 c.168C>T synonymous_variant 0.13
panD 4044225 p.Asp19Glu missense_variant 0.15
panD 4044232 p.Cys17Phe missense_variant 0.15
panD 4044444 c.-163G>T upstream_gene_variant 0.13
embC 4239704 c.-159C>T upstream_gene_variant 0.13
embC 4240657 c.795G>T synonymous_variant 0.13
embC 4240702 c.840G>T synonymous_variant 0.12
embC 4241135 p.Val425Leu missense_variant 0.18
embC 4241419 c.1557C>T synonymous_variant 0.33
embC 4241658 p.Ser599* stop_gained 0.5
embC 4242157 p.Met765Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242744 p.Thr961Lys missense_variant 0.2
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243423 p.Ser64Phe missense_variant 0.13
embA 4243483 p.Ala84Gly missense_variant 0.11
embA 4243941 p.Leu237Met missense_variant 0.2
embA 4243971 p.Gly247* stop_gained 0.2
embA 4244343 p.Ala371Thr missense_variant 0.14
embA 4244501 c.1269G>A synonymous_variant 0.22
embA 4244564 c.1332G>T synonymous_variant 0.29
embA 4244708 c.1476C>A synonymous_variant 0.14
embA 4245160 p.Ser643Ile missense_variant 0.15
embA 4245822 p.Pro864Ser missense_variant 0.14
embA 4245945 p.Ile905Val missense_variant 0.14
embB 4246605 p.Thr31Asn missense_variant 0.25
embB 4246958 p.Glu149* stop_gained 0.15
embB 4247184 p.Gly224Val missense_variant 0.12
embB 4247395 c.882C>A synonymous_variant 0.13
embB 4247487 p.Ser325Asn missense_variant 0.13
embB 4247595 p.Cys361Phe missense_variant 0.33
embB 4248160 p.Cys549* stop_gained 0.17
embB 4249009 c.2496G>C synonymous_variant 0.14
embB 4249527 p.Gly1005Asp missense_variant 0.2
aftB 4267250 p.Asp529Glu missense_variant 0.14
aftB 4268179 c.658T>C synonymous_variant 0.25
aftB 4268358 p.Gln160Arg missense_variant 0.2
aftB 4268681 c.155delG frameshift_variant 0.17
aftB 4268698 p.Pro47Ser missense_variant 0.14
ubiA 4269215 p.Arg207Cys missense_variant 0.25
aftB 4269495 c.-659G>T upstream_gene_variant 0.15
aftB 4269753 c.-917G>A upstream_gene_variant 0.17
ethA 4326019 c.1455C>A synonymous_variant 0.14
ethA 4326396 p.Gln360Lys missense_variant 0.25
ethA 4326758 p.Arg239Gln missense_variant 0.17
ethA 4327067 p.Leu136Arg missense_variant 1.0
ethR 4327204 c.-345G>T upstream_gene_variant 0.2
ethA 4327391 p.Pro28Leu missense_variant 0.25
ethR 4327636 p.Leu30Ile missense_variant 0.15
ethA 4327998 c.-525G>A upstream_gene_variant 0.18
ethA 4328424 c.-951C>A upstream_gene_variant 0.5
whiB6 4338319 p.Glu68Gly missense_variant 0.12
whiB6 4338397 p.Thr42Lys missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407816 c.387C>T synonymous_variant 0.13
gid 4407831 c.372G>T synonymous_variant 0.18
gid 4407851 p.Arg118Cys missense_variant 0.2
gid 4407877 p.Gly109Val missense_variant 0.22
gid 4408441 c.-239C>A upstream_gene_variant 0.2