TB-Profiler result

Run: ERR4813588
Summary

Run ID: ERR4813588

Sample name:

Date: 01-04-2023 12:51:39

Number of reads: 435389

Percentage reads mapped: 99.22

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 0.92
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 0.89 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9069 p.Thr590Ala missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576417 p.Leu357Arg missense_variant 0.33
rpoB 761745 p.Val647Leu missense_variant 0.22
rpoC 764921 p.Glu518* stop_gained 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ala 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
rpsA 1834683 p.Ala381Val missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918493 p.Phe185Cys missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726754 p.Gly188Cys missense_variant 0.22
Rv2752c 3064815 p.Asp459Glu missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086807 c.-13G>A upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475037 p.Val344Gly missense_variant 0.33
rpoA 3878630 c.-123G>C upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0