TB-Profiler result

Run: ERR4812999
Summary

Run ID: ERR4812999

Sample name:

Date: 01-04-2023 12:28:07

Number of reads: 189866

Percentage reads mapped: 99.42

Strain: lineage4

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
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 1.0 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 7824 p.Ala175Ser missense_variant 0.22
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8730 p.Gly477Trp missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9546 p.Gly749Cys missense_variant 0.22
gyrA 9659 c.2358C>A synonymous_variant 0.22
fgd1 490977 c.195C>A synonymous_variant 0.5
rpoB 762021 p.Asp739Tyr missense_variant 0.25
rpoB 762640 p.Gly945Val missense_variant 0.33
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ala missense_variant 1.0
mmpL5 776952 p.Leu510Pro missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473384 n.-274A>C upstream_gene_variant 0.33
rpsA 1833404 c.-138G>T upstream_gene_variant 0.4
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Ala missense_variant 0.67
katG 2156450 c.-339T>C upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726500 p.Leu103His missense_variant 0.25
ribD 2987159 p.Gln107His missense_variant 0.67
Rv2752c 3065558 c.633delC frameshift_variant 0.22
Rv2752c 3066038 p.His52Tyr missense_variant 0.33
thyX 3067377 p.Arg190Gln missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073938 c.534C>A synonymous_variant 0.2
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 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embB 4246764 p.Pro84Gln missense_variant 0.67
embB 4248797 p.Gly762Cys missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0