TB-Profiler result

Run: SRR23311002
Summary

Run ID: SRR23311002

Sample name:

Date: 14-03-2023 06:24:08

Number of reads: 2988922

Percentage reads mapped: 99.5

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 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.99 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embA 4243217 c.-16C>T upstream_gene_variant 0.95 ethambutol
embB 4247402 p.Ser297Ala missense_variant 0.99 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 576113 p.Arg256Gly missense_variant 0.27
mshA 576613 c.1266A>C synonymous_variant 0.32
mshA 576616 c.1269G>C synonymous_variant 0.27
ccsA 619969 p.Val27Ile missense_variant 0.99
rpoC 764817 p.Val483Gly 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 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.23
pepQ 2860157 p.Ala87Gly missense_variant 0.26
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.69
fbiD 3339749 p.Val211Gly missense_variant 0.21
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.25
whiB7 3568428 c.252A>G synonymous_variant 0.28
whiB7 3568429 c.249C>G synonymous_variant 0.24
rpoA 3878597 c.-90G>C upstream_gene_variant 0.5
rpoA 3878641 c.-134C>G upstream_gene_variant 0.46
embC 4240409 p.Pro183Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4249594 c.3081G>A synonymous_variant 0.97
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0