TB-Profiler result

Run: SRR1186993
Summary

Run ID: SRR1186993

Sample name:

Date: 03-04-2023 05:21:42

Number of reads: 758654

Percentage reads mapped: 98.62

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.14 streptomycin
katG 2155276 p.Gly279Asp missense_variant 0.13 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9162 p.Pro621Thr missense_variant 0.13
gyrA 9224 c.1923C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.24
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760337 c.531C>A synonymous_variant 0.12
rpoB 761096 c.1290G>A synonymous_variant 0.14
rpoB 761627 c.1821C>A synonymous_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765837 p.Leu823Pro missense_variant 0.12
rpoC 766281 p.Ser971Asn missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775658 p.Gln941His missense_variant 0.13
mmpL5 777142 p.Val447Met missense_variant 0.15
mmpL5 777237 p.Tyr415Phe missense_variant 0.15
mmpL5 778960 c.-480G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303115 p.Ala62Val missense_variant 0.15
fbiC 1304301 c.1371C>A synonymous_variant 0.15
fbiC 1305318 c.2388C>A synonymous_variant 0.12
fbiC 1305417 c.2487C>G synonymous_variant 0.12
Rv1258c 1406192 c.1149G>A synonymous_variant 0.13
Rv1258c 1406534 c.807C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472177 n.332C>A non_coding_transcript_exon_variant 0.14
rrl 1473764 n.107G>A non_coding_transcript_exon_variant 0.25
rrl 1473796 n.139T>C non_coding_transcript_exon_variant 0.22
rrl 1475028 n.1371G>T non_coding_transcript_exon_variant 0.13
rrl 1475360 n.1703G>T non_coding_transcript_exon_variant 0.33
rrl 1475619 n.1962C>A non_coding_transcript_exon_variant 0.25
rrl 1476265 n.2608G>T non_coding_transcript_exon_variant 0.29
rrl 1476339 n.2682G>T non_coding_transcript_exon_variant 0.25
rrl 1476453 n.2796C>A non_coding_transcript_exon_variant 0.13
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.12
inhA 1673790 c.-412C>T upstream_gene_variant 0.14
fabG1 1673902 p.Ala155Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918516 p.Gly193Ser missense_variant 0.13
tlyA 1918593 c.654G>A synonymous_variant 0.12
PPE35 2169313 p.Thr434Ala missense_variant 0.1
PPE35 2169641 c.972G>T synonymous_variant 0.13
PPE35 2170210 p.Ala135Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726139 c.-54C>G upstream_gene_variant 0.1
ahpC 2726265 p.Lys25Gln missense_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.29
ahpC 2726341 p.Val50Gly missense_variant 0.25
ahpC 2726345 c.153C>T synonymous_variant 0.33
folC 2747672 c.-74G>A upstream_gene_variant 0.17
pepQ 2859923 p.Gly166Cys missense_variant 0.13
pepQ 2860101 c.318C>A synonymous_variant 0.15
Rv2752c 3065586 p.Asp202Glu missense_variant 0.11
Rv2752c 3065783 p.Gly137Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087404 c.585G>A synonymous_variant 0.14
ald 3087869 c.1050A>G synonymous_variant 0.1
fbiD 3339027 c.-91G>T upstream_gene_variant 0.14
Rv3083 3449566 p.Gly355Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641230 p.Arg230Cys missense_variant 0.12
fbiB 3642053 c.519G>A synonymous_variant 0.12
fbiB 3642846 p.Pro438Thr missense_variant 0.12
fbiB 3642866 p.Leu444Phe missense_variant 0.12
rpoA 3877599 p.Gln303His missense_variant 0.25
rpoA 3878491 p.Arg6His missense_variant 0.17
clpC1 4038498 p.Ser736Ile missense_variant 0.12
clpC1 4038536 c.2169C>A synonymous_variant 0.12
clpC1 4039292 c.1413C>A synonymous_variant 0.12
embC 4240570 c.708C>A synonymous_variant 0.12
embC 4240571 p.Gly237Trp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243386 p.Asp52Tyr missense_variant 0.12
embA 4243435 p.Arg68His missense_variant 0.12
embA 4244381 c.1149G>A synonymous_variant 0.13
embA 4245492 p.Pro754Thr missense_variant 0.12
embA 4245603 p.Gly791Trp missense_variant 0.14
embB 4249054 c.2541C>A synonymous_variant 0.12
aftB 4267980 p.Arg286Gln missense_variant 0.14
ethR 4327375 c.-174G>A upstream_gene_variant 0.2
ethA 4327728 c.-255C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338684 c.-163C>A upstream_gene_variant 0.17