TB-Profiler result

Run: ERR4799446
Summary

Run ID: ERR4799446

Sample name:

Date: 20-10-2023 03:49:07

Number of reads: 3657815

Percentage reads mapped: 99.63

Strain: lineage3.1.2.1

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.Asp435Val (1.00)
Isoniazid R fabG1 c.-15C>T (0.95), katG p.Thr380Ile (0.98)
Ethambutol R embB p.Gly406Ser (0.96)
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (0.98)
Moxifloxacin R gyrA p.Asp94Gly (0.98)
Ofloxacin R gyrA p.Asp94Gly (0.98)
Levofloxacin R gyrA p.Asp94Gly (0.98)
Ciprofloxacin R gyrA p.Asp94Gly (0.98)
Aminoglycosides R rrs n.1401A>G (0.27)
Amikacin R rrs n.1401A>G (0.27), eis c.-14C>T (0.24)
Capreomycin R rrs n.1401A>G (0.27)
Kanamycin R rrs n.1401A>G (0.27), eis c.-14C>T (0.24), eis c.-37G>T (0.31)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.95)
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 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.96
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.97
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 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.95 isoniazid, ethionamide
katG 2154973 p.Thr380Ile missense_variant 0.98 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.24 kanamycin, amikacin
eis 2715369 c.-37G>T upstream_gene_variant 0.31 kanamycin
embB 4247729 p.Gly406Ser missense_variant 0.96 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 0.96
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473908 n.251C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102127 c.915dupG frameshift_variant 0.11
ndh 2102366 c.674_676dupGCG conservative_inframe_insertion 0.26
katG 2154328 p.Arg595Leu missense_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 0.99
pncA 2289473 c.-232T>G upstream_gene_variant 0.98
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038743 c.1962G>A synonymous_variant 0.93
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0