TB-Profiler result

Run: SRR23310843
Summary

Run ID: SRR23310843

Sample name:

Date: 14-03-2023 00:07:50

Number of reads: 2722629

Percentage reads mapped: 99.55

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 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
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 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
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 576108 p.Ala254Gly missense_variant 0.34
mshA 576482 p.Val379Leu missense_variant 0.28
ccsA 619969 p.Val27Ile 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
rrl 1475290 n.1633A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
fbiA 3640390 c.-153A>G upstream_gene_variant 1.0
fbiA 3640520 c.-23G>A upstream_gene_variant 0.47
rpoA 3877960 p.Val183Gly missense_variant 1.0
rpoA 3878580 c.-74_-73insCA upstream_gene_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0