TB-Profiler result

Run: ERR10762289
Summary

Run ID: ERR10762289

Sample name:

Date: 31-03-2023 11:01:58

Number of reads: 4209757

Percentage reads mapped: 99.45

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 0.93
lineage4.2.1 Euro-American (TUR) H3;H4 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
rpsL 781822 p.Lys88Arg missense_variant 0.92 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.95 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.94 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 0.92 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.94 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.94 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.93
mshA 576108 p.Ala254Gly missense_variant 0.16
ccsA 619969 p.Val27Ile missense_variant 0.96
rpoC 764888 p.Leu507Val missense_variant 0.93
rpoC 766645 p.Glu1092Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.91
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.9
ald 3086742 c.-78A>C upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.8
fbiD 3339736 p.Thr207Ala missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.23
rpoA 3878637 c.-130G>C upstream_gene_variant 0.27
rpoA 3878641 c.-134C>G upstream_gene_variant 0.45
embC 4240409 p.Pro183Ala missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.37
embB 4249594 c.3081G>A synonymous_variant 0.94
aftB 4267647 p.Asp397Gly missense_variant 0.1
ethA 4328376 c.-903G>C upstream_gene_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0