TB-Profiler result

Run: SRR18715049
Summary

Run ID: SRR18715049

Sample name:

Date: 03-04-2023 20:16:41

Number of reads: 2149572

Percentage reads mapped: 97.33

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;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
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326426 c.1047dupT frameshift_variant 1.0 ethionamide, ethionamide
gid 4407865 c.337dupG 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 0.14
mshA 576456 p.Val370Gly missense_variant 0.21
mshA 576616 c.1269G>C synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168051 c.2562G>A synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.17
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ribD 2986875 p.Pro13Ser missense_variant 1.0
Rv2752c 3065854 p.Ala113Glu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.83
fbiD 3339749 p.Val211Gly missense_variant 0.29
fbiD 3339751 p.Ala212Pro missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.4
rpoA 3878597 c.-90G>C upstream_gene_variant 0.2
embC 4240409 p.Pro183Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.25
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0