TB-Profiler result

Run: SRR10380215
Summary

Run ID: SRR10380215

Sample name:

Date: 02-04-2023 17:30:49

Number of reads: 3694368

Percentage reads mapped: 99.54

Strain: lineage4.2.1;lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.35
lineage4.2 Euro-American H;T;LAM None 0.66
lineage4.1.2 Euro-American T;H None 0.33
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.64
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.38
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 0.74 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.62 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.74 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.59 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.56 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.64 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 0.6
fgd1 491591 p.Lys270Met missense_variant 0.34
mshA 575679 p.Asn111Ser missense_variant 0.32
mshA 576108 p.Ala254Gly missense_variant 0.21
ccsA 619969 p.Val27Ile missense_variant 0.61
rpoB 760115 c.309C>T synonymous_variant 0.31
rpoC 764817 p.Val483Gly missense_variant 0.69
rpoC 765150 p.Gly594Glu missense_variant 0.37
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
rpsA 1834675 c.1134C>T synonymous_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156219 c.-108A>T upstream_gene_variant 0.3
PPE35 2169879 p.Phe245Cys missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.34
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086742 c.-78A>C upstream_gene_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.54
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.15
rpoA 3878641 c.-134C>G upstream_gene_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.34
embA 4244849 c.1617C>T synonymous_variant 0.32
embB 4249594 c.3081G>A synonymous_variant 0.59
ethA 4326632 p.His281Pro missense_variant 0.65
ethA 4328376 c.-903G>C upstream_gene_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0