TB-Profiler result

Run: SRR14801569
Summary

Run ID: SRR14801569

Sample name:

Date: 03-04-2023 11:52:53

Number of reads: 1178136

Percentage reads mapped: 99.47

Strain: lineage4.2.1

Drug-resistance: Pre-XDR-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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
ald 3087252 c.436_437dupGC frameshift_variant 1.0 cycloserine
embB 4247402 p.Ser297Ala missense_variant 1.0 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 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576107 p.Ala254Thr missense_variant 0.12
mshA 576442 p.Cys365Trp missense_variant 0.22
mshA 576456 p.Val370Gly missense_variant 0.5
mshA 576477 p.Leu377Arg missense_variant 0.3
mshA 576613 c.1266A>C synonymous_variant 0.29
mshA 576616 c.1269G>C synonymous_variant 0.22
ccsA 619969 p.Val27Ile missense_variant 0.97
rpoB 760995 p.Arg397Trp missense_variant 0.11
rpoC 764367 p.Gly333Ala missense_variant 0.25
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.26
fabG1 1673558 p.His40Pro missense_variant 0.14
tlyA 1917922 c.-18A>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.19
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2169937 p.Asn226Tyr missense_variant 0.12
PPE35 2170065 p.Ala183Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.15
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ald 3086742 c.-78A>C upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 1.0
fbiD 3339751 p.Ala212Pro missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.29
whiB7 3568428 c.252A>G synonymous_variant 0.33
rpoA 3878637 c.-130G>C upstream_gene_variant 1.0
rpoA 3878640 c.-133G>C upstream_gene_variant 0.5
rpoA 3878641 c.-134C>G upstream_gene_variant 0.5
embC 4240409 p.Pro183Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>G upstream_gene_variant 0.97
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4246529 p.Ser6Arg missense_variant 0.5
embB 4248328 c.1815G>C synonymous_variant 0.33
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.98
whiB6 4338205 p.Val106Gly missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0