TB-Profiler result

Run: ERR2510445

Summary

Run ID: ERR2510445

Sample name:

Date: 20-10-2023 07:13:50

Number of reads: 2673539

Percentage reads mapped: 99.59

Strain: lineage3

Drug-resistance: Pre-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.Ser450Trp (1.00)
Isoniazid R fabG1 c.-15C>T (0.32), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.74), embB p.Gly406Asp (0.18)
Pyrazinamide R pncA c.390_391dupGG (0.75), pncA c.390_391dupGG (0.75), pncA p.Asp63His (0.23)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.81), gyrA p.Asp94Gly (0.16)
Moxifloxacin R gyrA p.Ala90Val (0.81), gyrA p.Asp94Gly (0.16)
Ofloxacin R gyrA p.Ala90Val (0.81), gyrA p.Asp94Gly (0.16)
Levofloxacin R gyrA p.Ala90Val (0.81), gyrA p.Asp94Gly (0.16)
Ciprofloxacin R gyrA p.Ala90Val (0.81), gyrA p.Asp94Gly (0.16)
Aminoglycosides R rrs n.1401A>G (0.27)
Amikacin R rrs n.1401A>G (0.27)
Capreomycin R rrs n.1401A>G (0.27)
Kanamycin R rrs n.1401A>G (0.27)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.32)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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
gyrA 7570 p.Ala90Val missense_variant 0.81 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.32 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.75 pyrazinamide, pyrazinamide
pncA 2289055 p.Asp63His missense_variant 0.23 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.74 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.18 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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.96
rpoB 762051 p.His749Tyr missense_variant 0.38
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 765462 p.Asn698Ser missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778995 p.Ser2Arg missense_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473609 n.-49G>C upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.22
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 0.74
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247031 p.Arg173Leu missense_variant 0.22
whiB6 4338484 p.Asn13Ser missense_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0