TB-Profiler result

Run: SRR7592377

Summary

Run ID: SRR7592377

Sample name:

Date: 04-04-2023 19:51:19

Number of reads: 4295374

Percentage reads mapped: 99.32

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 0.08
lineage4.2 Euro-American H;T;LAM None 0.89
lineage4.1.2 Euro-American T;H None 0.12
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.87
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.06
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 0.92 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.91 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.9 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.86 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.86 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.93 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 0.84
fgd1 491591 p.Lys270Met missense_variant 0.12
ccsA 619969 p.Val27Ile missense_variant 0.93
rpoC 764817 p.Val483Gly missense_variant 0.88
rpoC 765150 p.Gly594Glu missense_variant 0.14
rpoC 767317 c.3948C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
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 0.82
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878653 c.-146A>C upstream_gene_variant 0.18
embA 4242553 c.-680G>C upstream_gene_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.14
embB 4249594 c.3081G>A synonymous_variant 0.84
ethA 4326632 p.His281Pro missense_variant 0.89
ethA 4328376 c.-903G>C upstream_gene_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0