TB-Profiler result

Run: SRR4033473

Summary

Run ID: SRR4033473

Sample name:

Date: 04-04-2023 06:07:17

Number of reads: 1313305

Percentage reads mapped: 99.61

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2155317 c.794delT frameshift_variant 0.11 isoniazid
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 5331 p.Gly31Asp missense_variant 0.12
gyrB 5520 p.Pro94Leu missense_variant 0.82
gyrB 5771 p.Ala178Thr missense_variant 0.18
gyrB 6528 p.Lys430Met missense_variant 0.18
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8645 c.1344C>T synonymous_variant 0.15
gyrA 8866 p.Glu522Gly missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9642 p.Gly781Arg missense_variant 0.12
fgd1 490621 c.-162C>G upstream_gene_variant 0.1
fgd1 490903 p.Phe41Leu missense_variant 0.25
fgd1 491427 c.645C>A synonymous_variant 0.22
fgd1 491460 p.Asp226Glu missense_variant 0.2
mshA 576102 p.Arg252Leu missense_variant 0.2
mshA 576217 p.Leu290Phe missense_variant 0.11
rpoB 760303 p.Glu166Gly missense_variant 0.11
rpoB 760409 c.603C>T synonymous_variant 0.18
rpoB 761674 p.Gly623Val missense_variant 0.14
rpoB 762413 p.Gln869His missense_variant 0.17
rpoB 763117 p.Glu1104Gly missense_variant 0.12
rpoC 763229 c.-141G>C upstream_gene_variant 0.12
rpoC 763679 p.Ile104Phe missense_variant 0.13
rpoC 763963 c.594C>T synonymous_variant 0.15
rpoC 764554 c.1185C>G synonymous_variant 0.33
rpoC 764603 c.1234C>A synonymous_variant 0.15
rpoC 764737 c.1368G>T synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765091 p.Leu574Phe missense_variant 0.17
rpoC 765776 p.Val803Ile missense_variant 0.13
rpoC 766016 p.Asp883Asn missense_variant 0.14
rpoC 766327 c.2958C>T synonymous_variant 0.14
rpoC 767317 c.3948C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775944 p.Val846Asp missense_variant 0.17
mmpL5 776143 c.2337delC frameshift_variant 0.17
mmpL5 776448 p.Glu678Gly missense_variant 0.12
mmpL5 777091 p.Val464Met missense_variant 0.12
mmpL5 777518 c.963G>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781584 p.Arg9Ser missense_variant 0.14
fbiC 1304363 p.Glu478Gly missense_variant 0.12
fbiC 1304735 p.Gln602Leu missense_variant 0.18
embR 1416385 c.963C>T synonymous_variant 0.18
embR 1417120 c.228G>T synonymous_variant 0.13
atpE 1461219 c.175T>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471664 n.-182C>T upstream_gene_variant 0.15
rrs 1471823 n.-22delT upstream_gene_variant 0.25
rrs 1472219 n.374T>C non_coding_transcript_exon_variant 0.33
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473011 n.1166G>A non_coding_transcript_exon_variant 0.22
rrl 1474559 n.902T>C non_coding_transcript_exon_variant 0.25
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 0.12
fabG1 1673614 p.Glu59Gln missense_variant 0.12
rpsA 1834386 c.848delC frameshift_variant 0.15
rpsA 1834508 c.970_971delTC frameshift_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917998 p.Arg20Pro missense_variant 0.12
tlyA 1918672 p.Thr245Ala missense_variant 0.13
katG 2154059 p.Gly685Cys missense_variant 0.18
katG 2154824 p.Leu430Met missense_variant 0.13
PPE35 2168100 p.Gln838Pro missense_variant 0.11
Rv1979c 2222162 p.Val335Ile missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288690 p.Cys184Trp missense_variant 0.15
pncA 2290059 c.-818T>G upstream_gene_variant 0.11
kasA 2518085 c.-30C>G upstream_gene_variant 0.12
kasA 2519053 c.939G>T synonymous_variant 0.14
kasA 2519169 p.Ala352Val missense_variant 0.22
kasA 2519299 c.1185C>T synonymous_variant 0.12
eis 2714853 c.480C>T synonymous_variant 0.14
eis 2714884 p.His150Arg missense_variant 0.12
ahpC 2726310 p.Ser40Gly missense_variant 0.12
ahpC 2726320 p.His43Arg missense_variant 0.12
folC 2746532 p.Pro356Leu missense_variant 0.17
folC 2747033 p.Ala189Val missense_variant 0.14
pepQ 2860360 p.Asp20Gly missense_variant 0.1
ribD 2987023 p.Met62Thr missense_variant 0.11
ribD 2987476 p.Leu213Arg missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339680 p.Asp188Val missense_variant 0.12
Rv3083 3448718 p.Val72Glu missense_variant 0.12
Rv3083 3449531 p.Val343Asp missense_variant 0.17
Rv3083 3449950 c.1447C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474379 p.Ala125Thr missense_variant 0.17
Rv3236c 3612394 c.723T>C synonymous_variant 0.14
fbiA 3640892 p.Gln117Leu missense_variant 0.17
fbiA 3640904 p.Ala121Val missense_variant 0.17
fbiB 3642636 p.Ala368Thr missense_variant 0.18
fbiB 3642650 p.Met372Ile missense_variant 0.15
fbiB 3642668 c.1134A>T synonymous_variant 0.17
fbiB 3642677 c.1143A>T synonymous_variant 0.15
alr 3841092 p.Leu110Pro missense_variant 0.12
rpoA 3877539 c.969C>T synonymous_variant 0.18
rpoA 3878137 p.His124Arg missense_variant 0.18
ddn 3987202 p.Ala120Val missense_variant 0.15
clpC1 4038232 p.Lys825Glu missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4043916 c.366A>T synonymous_variant 0.15
panD 4044004 p.Met93Thr missense_variant 0.18
panD 4044109 p.Tyr58Ser missense_variant 0.11
embC 4240678 c.816T>C synonymous_variant 0.13
embC 4241391 p.Leu510Pro missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242957 p.Pro1032Gln missense_variant 0.14
embA 4244526 p.Leu432Met missense_variant 0.13
embA 4244539 p.Ala436Glu missense_variant 0.14
embB 4246175 c.-339C>T upstream_gene_variant 0.17
embB 4246693 c.180G>A synonymous_variant 0.17
embB 4246713 p.Val67Ala missense_variant 0.13
embB 4246983 p.Thr157Ile missense_variant 0.13
embB 4249530 p.Ile1006Asn missense_variant 0.15
aftB 4267425 p.Gly471Glu missense_variant 0.13
aftB 4268774 p.Ser21Arg missense_variant 0.15
ubiA 4269050 p.Tyr262Asn missense_variant 0.12
ubiA 4269135 p.Tyr233* stop_gained 0.12
ethR 4327613 p.Gly22Val missense_variant 0.22
ethA 4328251 c.-778G>A upstream_gene_variant 0.13
ethA 4328389 c.-916C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338718 c.-197C>T upstream_gene_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0