TB-Profiler result

Run: ERR4872300
Summary

Run ID: ERR4872300

Sample name:

Date: 01-04-2023 21:31:43

Number of reads: 4380388

Percentage reads mapped: 99.44

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 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
gyrA 7582 p.Asp94Gly 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 0.99 isoniazid
pncA 2289231 p.Leu4Ser missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4248003 p.Gln497Arg 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.28
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoB 762310 p.His835Arg missense_variant 1.0
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
fabG1 1673553 p.Asp38Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.82
fbiD 3339746 p.Ala210Gly missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.24
alr 3841356 p.Ser22Leu missense_variant 1.0
rpoA 3878613 c.-106A>C upstream_gene_variant 0.14
rpoA 3878641 c.-134C>G upstream_gene_variant 0.48
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 0.99
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0