TB-Profiler result

Run: SRR14782478
Summary

Run ID: SRR14782478

Sample name:

Date: 03-04-2023 11:27:18

Number of reads: 1312321

Percentage reads mapped: 99.39

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 1.0
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.96
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 0.94 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.91 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289212 p.Gln10His missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.94 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.95 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 0.97
gyrA 9647 c.2346C>G synonymous_variant 0.19
fgd1 491247 c.465C>T synonymous_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576479 p.Pro378Ala missense_variant 0.13
ccsA 619969 p.Val27Ile missense_variant 0.96
rpoC 764367 p.Gly333Ala missense_variant 0.21
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
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 0.96
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289211 p.Asn11Tyr missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.19
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.2
rpoA 3878641 c.-134C>G upstream_gene_variant 0.38
embC 4240409 p.Pro183Ala missense_variant 0.12
embC 4240413 p.Leu184Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.23
embB 4248324 p.Ala604Gly missense_variant 0.26
embB 4248328 c.1815G>C synonymous_variant 0.24
embB 4249594 c.3081G>A synonymous_variant 0.9
ubiA 4269721 p.Ala38Val missense_variant 0.91
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0