TB-Profiler result

Run: ERR6336801
Summary

Run ID: ERR6336801

Sample name:

Date: 02-04-2023 02:03:54

Number of reads: 573965

Percentage reads mapped: 99.02

Strain: lineage1.2.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918473 c.536delC frameshift_variant 0.2 capreomycin
thyA 3074095 p.Arg126Gln missense_variant 0.22 para-aminosalicylic_acid
gid 4407796 p.Ser136* stop_gained 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 5963 p.Ala242Thr missense_variant 0.2
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7369 p.Glu23Gly missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8303 p.His334Gln missense_variant 0.15
gyrA 8442 p.Leu381Val missense_variant 0.2
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Ile missense_variant 0.15
fgd1 491511 p.Leu243Phe missense_variant 0.17
fgd1 491513 p.Asn244Ser missense_variant 0.18
fgd1 491516 p.Asn245Ser missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575175 c.-173G>A upstream_gene_variant 0.14
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575714 p.Tyr123His missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576289 c.942G>A synonymous_variant 0.15
mshA 576721 p.Glu458Asp missense_variant 0.2
mshA 576738 p.Val464Gly missense_variant 0.22
ccsA 620616 c.726C>T synonymous_variant 0.15
rpoB 759775 c.-32G>A upstream_gene_variant 0.13
rpoB 760717 p.Arg304His missense_variant 0.12
rpoB 761749 p.Ser648Leu missense_variant 0.18
rpoB 762945 p.Thr1047Ala missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763247 c.-123G>A upstream_gene_variant 0.12
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763659 p.Leu97Pro missense_variant 0.11
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765055 c.1686C>T synonymous_variant 0.14
rpoC 766089 p.Asp907Ala missense_variant 0.29
rpoC 766142 c.2773C>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777403 p.Val360Met missense_variant 0.22
mmpS5 778736 p.Glu57Gly missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781667 c.108C>T synonymous_variant 0.12
rpsL 781750 p.Thr64Met missense_variant 0.17
rplC 801303 c.495G>A synonymous_variant 0.13
rplC 801410 p.Arg201His missense_variant 0.17
rplC 801441 c.633G>A synonymous_variant 0.15
fbiC 1304358 c.1428C>T synonymous_variant 0.13
Rv1258c 1406308 p.Arg345Gly missense_variant 0.13
Rv1258c 1406674 p.Arg223Trp missense_variant 0.17
Rv1258c 1407394 c.-54C>T upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417082 p.Asp89Gly missense_variant 0.18
embR 1417169 c.177_178delCT frameshift_variant 0.12
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461078 p.Gly12Ser missense_variant 0.12
atpE 1461130 p.Gly29Asp missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 1.0
rrs 1472759 n.914T>A non_coding_transcript_exon_variant 0.12
rrs 1473219 n.1374T>C non_coding_transcript_exon_variant 0.11
rrl 1474060 n.403G>A non_coding_transcript_exon_variant 0.14
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
fabG1 1673986 p.Pro183Ser missense_variant 0.18
inhA 1674484 p.Ile95Leu missense_variant 1.0
rpsA 1833840 p.Leu100Pro missense_variant 0.12
rpsA 1834249 c.708T>C synonymous_variant 0.15
tlyA 1917823 c.-117C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102398 c.645C>T synonymous_variant 0.22
katG 2154037 p.Ser692Thr missense_variant 0.43
katG 2154043 p.Thr690Asn missense_variant 0.25
katG 2154174 c.1938C>T synonymous_variant 0.17
katG 2154255 c.1857C>T synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168417 c.2196C>T synonymous_variant 0.18
Rv1979c 2222249 p.Val306Ile missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222640 c.525G>A synonymous_variant 0.15
Rv1979c 2222737 p.Gly143Asp missense_variant 0.15
Rv1979c 2222839 p.Leu109Ser missense_variant 0.15
Rv1979c 2223105 c.60C>T synonymous_variant 0.13
Rv1979c 2223204 c.-40T>C upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289234 p.Ala3Val missense_variant 0.12
pncA 2289237 p.Arg2Gln missense_variant 0.12
pncA 2289884 c.-644_-643insA upstream_gene_variant 0.22
pncA 2290073 c.-832T>C upstream_gene_variant 0.18
pncA 2290196 c.-955A>G upstream_gene_variant 0.11
kasA 2517954 c.-161G>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518397 c.286delG frameshift_variant 0.12
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519188 c.1074G>A synonymous_variant 0.18
eis 2714858 p.Gly159Ser missense_variant 0.33
ahpC 2725962 c.-231C>T upstream_gene_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746530 p.Ala357Thr missense_variant 0.29
folC 2747462 p.Ser46Asn missense_variant 0.14
pepQ 2859568 p.Ala284Val missense_variant 0.15
pepQ 2859768 p.Phe217Leu missense_variant 0.14
ribD 2987206 p.Ser123Cys missense_variant 0.13
ribD 2987571 p.Thr245Ser missense_variant 0.18
Rv2752c 3064552 p.Arg547His missense_variant 0.18
Rv2752c 3065212 p.Thr327Met missense_variant 0.2
Rv2752c 3066286 c.-95C>T upstream_gene_variant 0.13
thyA 3074162 p.Pro104Ser missense_variant 0.33
thyA 3074245 p.Gly76Glu missense_variant 0.17
thyA 3074407 p.Thr22Ile missense_variant 0.12
thyA 3074497 c.-26G>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087350 c.531C>G synonymous_variant 0.13
ald 3087414 p.Ile199Phe missense_variant 0.13
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.23
fbiD 3339744 c.627A>C synonymous_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448748 p.Arg82Gln missense_variant 0.14
Rv3083 3448996 p.His165Tyr missense_variant 0.14
Rv3083 3449025 p.Asp174Glu missense_variant 0.12
Rv3083 3449295 c.792G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474700 p.Gly232Ser missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475192 p.Lys396Glu missense_variant 0.13
fprA 3475344 p.Ser446Arg missense_variant 0.25
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612568 c.549G>A synonymous_variant 0.25
Rv3236c 3612776 p.Asp114Val missense_variant 0.13
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641104 p.Val188Phe missense_variant 1.0
fbiB 3642501 p.Ser323Arg missense_variant 0.21
alr 3840829 p.Val198Ile missense_variant 0.17
alr 3841222 p.Ala67Thr missense_variant 0.12
rpoA 3877837 p.Glu224Ala missense_variant 0.11
rpoA 3878483 c.25C>T synonymous_variant 0.12
rpoA 3878501 p.Ile3Phe missense_variant 0.14
clpC1 4040338 p.Val123Met missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240411 c.549G>C synonymous_variant 0.22
embC 4240553 p.Met231Leu missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240841 p.Tyr327His missense_variant 0.11
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241046 p.Gly395Val missense_variant 0.29
embC 4241822 p.Phe654Ile missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243751 c.519C>T synonymous_variant 0.15
embA 4244132 c.900G>A synonymous_variant 0.15
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244491 p.Thr420Met missense_variant 0.4
embA 4245218 c.1986C>T synonymous_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4247322 p.Pro270Leu missense_variant 0.25
embB 4247424 p.Leu304Pro missense_variant 0.12
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248319 c.1806A>T synonymous_variant 0.33
embB 4248753 p.Cys747Tyr missense_variant 0.15
embB 4249354 c.2841G>A synonymous_variant 0.13
aftB 4268296 p.Cys181Arg missense_variant 0.13
aftB 4268367 p.Cys157Tyr missense_variant 0.13
aftB 4269231 c.-395C>T upstream_gene_variant 0.17
aftB 4269267 c.-431C>T upstream_gene_variant 0.18
ubiA 4269325 c.508delA frameshift_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269505 p.Gly110Glu missense_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338325 p.Ala66Gly missense_variant 0.12
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338443 p.Tyr27His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408174 p.Ala10Gly missense_variant 0.11