TB-Profiler result

Run: ERR2679261
Summary

Run ID: ERR2679261

Sample name:

Date: 31-03-2023 23:00:34

Number of reads: 269167

Percentage reads mapped: 99.49

Strain: lineage4.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;X;H None 0.99
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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288746 c.495delC frameshift_variant 0.9 pyrazinamide, pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.89 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.94 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
gyrA 9557 c.2256G>C synonymous_variant 1.0
fgd1 490605 c.-178G>A upstream_gene_variant 0.15
fgd1 490929 c.147C>A synonymous_variant 0.17
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
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
rpsL 781765 p.Gly69Asp missense_variant 0.11
fbiC 1303818 c.888C>A synonymous_variant 0.22
fbiC 1304610 c.1680C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 0.13
PPE35 2167814 p.Tyr933* stop_gained 0.11
PPE35 2170002 p.Ala204Asp missense_variant 0.14
PPE35 2170749 c.-137A>G upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223354 c.-190A>G upstream_gene_variant 0.11
pncA 2288841 p.Ala134Gly missense_variant 0.22
eis 2714889 c.444C>T synonymous_variant 0.2
Rv2752c 3065536 p.Gly219Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449153 p.Ile217Thr missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474775 p.Asp257Tyr missense_variant 0.17
fprA 3475244 p.Arg413His missense_variant 0.18
rpoA 3878245 p.Glu88Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
aftB 4269835 c.-999G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338661 c.-140C>T upstream_gene_variant 1.0