TB-Profiler result

Run: ERR4812359
Summary

Run ID: ERR4812359

Sample name:

Date: 01-04-2023 12:01:40

Number of reads: 3474481

Percentage reads mapped: 99.73

Strain: lineage4.3.3;lineage4.1.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.4
lineage4.1 Euro-American T;X;H None 0.56
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.61
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.45
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 0.56 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.38 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.38 ethambutol
gid 4407952 p.Pro84Leu missense_variant 0.44 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
gyrB 5858 p.Asn207Asp missense_variant 0.55
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576111 p.Ala255Gly missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 0.39
rpoC 765150 p.Gly594Glu missense_variant 0.52
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
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.4
tlyA 1917792 c.-148G>A upstream_gene_variant 0.49
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290113 c.-872G>A upstream_gene_variant 0.54
kasA 2518919 p.Gly269Ser missense_variant 0.39
thyA 3073868 p.Thr202Ala missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.44
embC 4242182 p.Ala774Ser missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.56
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4248555 p.Gly681Asp missense_variant 0.58
embB 4249408 c.2895G>A synonymous_variant 0.58
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.35