TB-Profiler result

Run: ERR11003793
Summary

Run ID: ERR11003793

Sample name:

Date: 31-03-2023 11:25:31

Number of reads: 1952387

Percentage reads mapped: 99.45

Strain: lineage4.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.98
lineage4.2 Euro-American H;T;LAM None 0.94
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.95
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 0.92 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.94 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 0.12 pyrazinamide
pncA 2288820 p.Gln141Pro missense_variant 0.93 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.93 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.91 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 0.88
fgd1 491742 c.960T>C synonymous_variant 0.1
ccsA 619969 p.Val27Ile missense_variant 0.92
rpoC 764817 p.Val483Gly missense_variant 0.96
rpoC 764916 p.Leu516Pro missense_variant 0.17
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 1673380 c.-60C>G upstream_gene_variant 0.14
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 0.95
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
embB 4249594 c.3081G>A synonymous_variant 0.93
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0