TB-Profiler result

Run: SRR18002879
Summary

Run ID: SRR18002879

Sample name:

Date: 03-04-2023 19:07:31

Number of reads: 4124895

Percentage reads mapped: 88.89

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 0.94
lineage4.4 Euro-American S;T None 0.92
lineage4.4.2 Euro-American T1;T2 None 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 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288740 p.Thr168Pro missense_variant 0.93 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.87 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.96 ethambutol
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 575254 c.-94C>T upstream_gene_variant 0.93
mshA 576108 p.Ala254Gly missense_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
rpoC 764724 p.Phe452Cys missense_variant 0.95
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
katG 2155854 c.258C>A synonymous_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.95
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.21
embB 4247249 p.Gly246Arg missense_variant 0.95
aftB 4267647 p.Asp397Gly missense_variant 0.12
aftB 4268928 c.-92C>T upstream_gene_variant 0.92
aftB 4269375 c.-539G>A upstream_gene_variant 0.95
ethA 4327058 p.Gly139Val missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407712 p.Gly164Ala missense_variant 0.94