TB-Profiler result

Run: SRR671725
Summary

Run ID: SRR671725

Sample name:

Date: 04-04-2023 15:25:16

Number of reads: 5608809

Percentage reads mapped: 99.41

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 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 761155 p.Ser450Leu missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Asn missense_variant 0.99 isoniazid
pncA 2289072 p.His57Arg missense_variant 0.99 pyrazinamide
embA 4243217 c.-16C>G upstream_gene_variant 0.98 ethambutol
ethA 4326699 c.774delG frameshift_variant 0.93 ethionamide, ethionamide
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
mshA 576585 p.Arg413Gln missense_variant 0.99
rpoC 762836 c.-534C>G upstream_gene_variant 0.19
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.27
Rv2752c 3064552 p.Arg547Pro missense_variant 0.2
Rv2752c 3066099 p.Met31Ile missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
embC 4240654 c.792C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.37
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4248320 p.Gly603Arg missense_variant 0.99
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0