TB-Profiler result

Run: ERR3335743
Summary

Run ID: ERR3335743

Sample name:

Date: 21-10-2023 14:59:24

Number of reads: 7434733

Percentage reads mapped: 99.43

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.Ser450Leu (0.94)
Isoniazid R katG p.Ser315Thr (0.91)
Ethambutol R embB p.Met306Val (0.93)
Pyrazinamide
Streptomycin R rrs n.878G>A (0.93)
Fluoroquinolones R gyrA p.Asp94Gly (0.95)
Moxifloxacin R gyrA p.Asp94Gly (0.95)
Ofloxacin R gyrA p.Asp94Gly (0.95)
Levofloxacin R gyrA p.Asp94Gly (0.95)
Ciprofloxacin R gyrA p.Asp94Gly (0.95)
Aminoglycosides
Amikacin R eis c.-14C>T (0.90)
Capreomycin
Kanamycin R eis c.-14C>T (0.90)
Cycloserine
Ethionamide
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 7582 p.Asp94Gly missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.93 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.9 kanamycin, amikacin
embB 4247429 p.Met306Val 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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoB 759786 c.-21G>C upstream_gene_variant 0.94
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Gln missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471647 n.-199G>T upstream_gene_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288757 p.Gly162Val missense_variant 0.91
pncA 2289047 c.195C>T synonymous_variant 0.96
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074303 p.Tyr57Asn missense_variant 0.52
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641802 p.Asp90Asn missense_variant 0.87
alr 3841473 c.-53G>A upstream_gene_variant 0.95
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326756 p.Trp240Arg missense_variant 0.94
whiB6 4338594 c.-73T>A upstream_gene_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407733 p.Gly157Ala missense_variant 0.95
gid 4408010 p.Val65Phe missense_variant 0.95
gid 4408107 p.Glu32Asp missense_variant 0.96