TB-Profiler result

Run: SRR7517681
Summary

Run ID: SRR7517681

Sample name:

Date: 04-04-2023 19:31:25

Number of reads: 1429980

Percentage reads mapped: 99.14

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 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289200 p.Cys14Trp missense_variant 1.0 pyrazinamide
gid 4407967 p.Leu79Ser missense_variant 1.0 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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776186 p.Phe765Leu missense_variant 0.14
mmpS5 778764 p.Pro48Thr missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471783 n.-63C>A upstream_gene_variant 0.12
rrs 1472736 n.891G>T non_coding_transcript_exon_variant 0.12
rpsA 1833555 p.Thr5Asn missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102909 p.Arg45Leu missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641206 p.Ala222Ser missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243204 c.-28delT upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.1
embB 4248027 p.Ala505Val missense_variant 1.0
ethA 4326260 p.Leu405Ser missense_variant 0.11
ethA 4327425 p.Val17Ile missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0