TB-Profiler result

Run: SRR6785147
Summary

Run ID: SRR6785147

Sample name:

Date: 04-04-2023 15:32:49

Number of reads: 1358555

Percentage reads mapped: 99.41

Strain: lineage4.2.1.1

Drug-resistance: Other

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
gid 4408065 c.137dupA frameshift_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 761347 p.Val514Gly missense_variant 0.25
rpoC 765237 p.Asp623Ala missense_variant 0.17
rpoC 766644 p.Glu1092Gly missense_variant 0.2
rpoC 767155 c.3786C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777219 p.Leu421Gln missense_variant 0.67
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407039 p.Val101Gly missense_variant 0.15
Rv1258c 1407253 p.Phe30Val missense_variant 1.0
embR 1417392 c.-45A>C upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1833765 p.Asp75Ala missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102386 c.657G>A synonymous_variant 0.25
PPE35 2169219 p.Leu465Arg missense_variant 0.4
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449220 c.717C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4239883 c.21A>C synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.2
embC 4243092 p.Leu1077Arg missense_variant 0.18
embC 4243095 p.Gly1078Val missense_variant 0.18
embA 4243099 c.-134G>C upstream_gene_variant 0.18
embA 4243102 c.-131G>T upstream_gene_variant 0.18
embC 4243103 p.Thr1081Pro missense_variant 0.18
embC 4243106 p.Arg1082Ser missense_variant 0.18
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.18
embA 4243470 p.Ala80Ser missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.25
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
ethR 4327755 p.Glu69Asp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0