TB-Profiler result

Run: SRR10380086
Summary

Run ID: SRR10380086

Sample name:

Date: 02-04-2023 17:26:25

Number of reads: 1385826

Percentage reads mapped: 99.39

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 0.94
lineage4.2 Euro-American H;T;LAM None 0.93
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.94
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 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.93 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.95 isoniazid, ethionamide
inhA 1674048 c.-154G>A upstream_gene_variant 0.11 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.94 kanamycin
folC 2747151 p.Ser150Gly missense_variant 0.11 para-aminosalicylic_acid
embB 4247402 p.Ser297Ala missense_variant 0.88 ethambutol
embB 4247429 p.Met306Val missense_variant 0.12 ethambutol
ethA 4326705 c.768delG frameshift_variant 0.17 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.18
ccsA 619969 p.Val27Ile missense_variant 0.96
ccsA 620625 p.Ile245Met missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.12
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 2169879 p.Phe245Cys missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.93
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 4243460 c.228C>T synonymous_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.22
embB 4249594 c.3081G>A synonymous_variant 0.9
ethA 4326632 p.His281Pro missense_variant 0.88
ethA 4328376 c.-903G>C upstream_gene_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.13