TB-Profiler result

Run: ERR2510478
Summary

Run ID: ERR2510478

Sample name:

Date: 20-10-2023 07:06:13

Number of reads: 1931297

Percentage reads mapped: 99.51

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.His445Tyr (0.25), rpoB p.Ser450Leu (0.71)
Isoniazid R fabG1 c.-8T>A (0.78), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (0.79)
Pyrazinamide R pncA p.Trp68Gly (0.83)
Streptomycin R rpsL p.Lys43Arg (0.15), rrs n.906A>G (0.87), gid p.Pro75Arg (0.91)
Fluoroquinolones R gyrA p.Asp94Asn (0.72)
Moxifloxacin R gyrA p.Asp94Asn (0.72)
Ofloxacin R gyrA p.Asp94Asn (0.72)
Levofloxacin R gyrA p.Asp94Asn (0.72)
Ciprofloxacin R gyrA p.Asp94Asn (0.72)
Aminoglycosides R rrs n.1401A>G (0.76)
Amikacin R rrs n.1401A>G (0.76)
Capreomycin R rrs n.1401A>G (0.76)
Kanamycin R rrs n.1401A>G (0.76)
Cycloserine
Ethionamide R ethA c.382dupG (0.84), ethA c.382dupG (0.84)
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 7581 p.Asp94Asn missense_variant 0.72 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.25 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.71 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.15 streptomycin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.87 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.76 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.78 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 0.83 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.79 ethambutol
ethA 4327091 c.382dupG frameshift_variant 0.84 ethionamide, ethionamide
gid 4407979 p.Pro75Arg missense_variant 0.91 streptomycin
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 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 0.81
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 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.3
rrl 1476436 n.2779A>G non_coding_transcript_exon_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156467 c.-356T>G upstream_gene_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3066026 c.165delC frameshift_variant 0.85
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338924 c.-194C>T upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612743 p.Thr125Ser missense_variant 0.78
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.2
embA 4243218 c.-15C>G upstream_gene_variant 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0