TB-Profiler result

Run: ERR4813295

Summary

Run ID: ERR4813295

Sample name:

Date: 01-04-2023 12:39:48

Number of reads: 2289737

Percentage reads mapped: 99.52

Strain: lineage4.3.3

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 0.99 pyrazinamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619993 p.Glu35* stop_gained 0.5
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304029 p.Pro367Ser missense_variant 0.13
Rv1258c 1407089 c.252G>A synonymous_variant 0.4
Rv1258c 1407126 p.Arg72Leu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917977 p.Arg13Gln missense_variant 0.22
PPE35 2170011 p.Arg201Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyX 3067220 c.726G>T synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642136 p.Ala201Asp missense_variant 0.2
fbiB 3642230 c.696G>A synonymous_variant 0.2
alr 3841073 c.348C>T synonymous_variant 0.18
clpC1 4038185 c.2520G>T synonymous_variant 0.17
clpC1 4038193 p.His838Tyr missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244336 p.Phe368Leu missense_variant 0.12
embB 4247139 p.Arg209Gln missense_variant 0.15
embB 4247806 c.1293G>T synonymous_variant 0.14
embB 4247929 c.1416G>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0