TB-Profiler result

Run: SRR7585421
Summary

Run ID: SRR7585421

Sample name:

Date: 04-04-2023 19:46:45

Number of reads: 1973721

Percentage reads mapped: 85.61

Strain: lineage4.4

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 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 761140 p.His445Leu missense_variant 1.0 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.97 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327053 c.410_420dupGCAGCGGCTAC frameshift_variant 1.0 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 8006 c.705C>G synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762004 p.Asn733Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779003 p.Asp5Ala 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 2170558 p.Ala19Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714523 p.His270Gln missense_variant 1.0
Rv2752c 3065715 c.477T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243324 p.Val31Ala missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
embB 4247548 c.1035C>T synonymous_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.13
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407712 p.Gly164Asp missense_variant 1.0