TB-Profiler result

Run: SRR6257080
Summary

Run ID: SRR6257080

Sample name:

Date: 04-04-2023 13:25:33

Number of reads: 726644

Percentage reads mapped: 100.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288953 p.Gly97Ser missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
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 6208 c.969G>T synonymous_variant 0.17
gyrB 7025 p.Lys596Glu missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9140 p.Gln613His missense_variant 0.12
rpoB 759915 p.Lys37Glu missense_variant 0.11
rpoC 767309 p.Asp1314Tyr missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801227 p.Gly140Val missense_variant 0.14
Rv1258c 1407094 p.Gly83Cys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472818 n.973C>T non_coding_transcript_exon_variant 1.0
rrl 1473934 n.277G>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475226 n.1569C>A non_coding_transcript_exon_variant 0.22
fabG1 1673155 c.-285G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154619 p.Arg498Leu missense_variant 0.15
katG 2154654 p.Ser486Arg missense_variant 0.13
katG 2155430 p.Ile228Leu missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169830 p.Asn261Lys missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518693 c.579C>A synonymous_variant 0.15
eis 2714397 p.His312Gln missense_variant 0.11
folC 2746724 p.Pro292Leu missense_variant 0.11
Rv2752c 3067004 c.-813C>A upstream_gene_variant 0.12
thyX 3067913 c.33G>T synonymous_variant 0.12
thyX 3067921 p.Val9Leu missense_variant 0.12
thyA 3074422 p.Pro17Leu missense_variant 1.0
thyA 3074598 c.-127A>G upstream_gene_variant 0.15
ald 3087248 p.Gln143His missense_variant 0.13
ald 3087302 c.483C>A synonymous_variant 0.12
fbiD 3339701 p.Leu195Pro missense_variant 0.12
fbiB 3642748 p.Ala405Asp missense_variant 0.17
clpC1 4038197 c.2508A>G synonymous_variant 0.13
clpC1 4038902 c.1803C>T synonymous_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243770 p.Gly180* stop_gained 0.12
embA 4243793 c.561C>A synonymous_variant 0.12
embA 4245994 p.Ala921Glu missense_variant 0.12
embB 4247693 p.Ala394Ser missense_variant 0.14
embB 4248036 p.Val508Gly missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.19
aftB 4268805 p.Thr11Lys missense_variant 0.12
ubiA 4269149 p.Val229Leu missense_variant 0.11
ubiA 4269864 c.-32delG upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Glu missense_variant 1.0