TB-Profiler result

Run: SRR25827362
Summary

Run ID: SRR25827362

Sample name:

Date: 15-03-2024 10:18:16

Number of reads: 8886678

Percentage reads mapped: 99.0

Strain: lineage3;lineage2.2.1

Drug-resistance: XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.93)
Isoniazid R fabG1 c.-15C>T (0.37), katG p.Ser315Thr (0.84)
Ethambutol R embA c.-12C>T (0.13), embB p.Gly406Ser (0.31), embB p.Gln497Arg (0.29)
Pyrazinamide R pncA p.Gly132Ala (0.62), pncA c.-11A>G (0.27)
Streptomycin R rpsL p.Lys43Arg (0.67)
Fluoroquinolones R gyrA p.Asp94Gly (0.84)
Moxifloxacin R gyrA p.Asp94Gly (0.84)
Ofloxacin R gyrA p.Asp94Gly (0.84)
Levofloxacin R gyrA p.Asp94Gly (0.84)
Ciprofloxacin R gyrA p.Asp94Gly (0.84)
Aminoglycosides R rrs n.1401A>G (0.53)
Amikacin R rrs n.1401A>G (0.53)
Capreomycin R rrs n.1401A>G (0.53)
Kanamycin R rrs n.1401A>G (0.53)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.37)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.17)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.26
lineage2 East-Asian Beijing RD105 0.79
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.74
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.78
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
gyrA 7582 p.Asp94Gly missense_variant 0.84 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.67 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.17 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.53 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.37 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.62 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.27 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.13 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.31 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.29 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
fgd1 491290 p.Val170Met missense_variant 0.82
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.76
ccsA 620625 p.Ile245Met missense_variant 0.82
rpoB 759746 c.-61C>T upstream_gene_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.76
mmpR5 779274 p.Leu95Phe missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.69
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.68
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.48
ahpC 2726105 c.-88G>A upstream_gene_variant 0.29
thyA 3074529 c.-58G>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475316 p.His437Pro missense_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8
embC 4241022 p.Ala387Val missense_variant 0.85
embC 4242075 p.Arg738Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.63
aftB 4267647 p.Asp397Gly missense_variant 0.8
aftB 4268753 c.84T>G synonymous_variant 0.35
ethA 4327051 p.Tyr141* stop_gained 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.81