TB-Profiler result

Run: ERR1034585
Summary

Run ID: ERR1034585

Sample name:

Date: 20-10-2023 22:00:37

Number of reads: 32600442

Percentage reads mapped: 99.44

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 (0.85)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.86), embB p.Asp1024Asn (0.83)
Pyrazinamide R pncA c.446_455dupATGGCTTGGC (0.72)
Streptomycin R rpsL p.Lys43Arg (0.85), gid c.102delG (0.17)
Fluoroquinolones R gyrA p.Asp94Tyr (0.88)
Moxifloxacin R gyrA p.Asp94Tyr (0.88)
Ofloxacin R gyrA p.Asp94Tyr (0.88)
Levofloxacin R gyrA p.Asp94Tyr (0.88)
Ciprofloxacin R gyrA p.Asp94Tyr (0.88)
Aminoglycosides R rrs n.1401A>G (0.89)
Amikacin R rrs n.1401A>G (0.89)
Capreomycin R rrs n.1401A>G (0.89)
Kanamycin R rrs n.1401A>G (0.89)
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 7581 p.Asp94Tyr missense_variant 0.88 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.85 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288786 c.446_455dupATGGCTTGGC frameshift_variant 0.72 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.86 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.83 ethambutol
gid 4408100 c.102delG frameshift_variant 0.17 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 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778801 c.-321A>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473635 n.-23A>G upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101965 p.Glu360Lys missense_variant 0.86
ndh 2102059 c.982_983dupGG frameshift_variant 0.82
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 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
folC 2747472 p.Ile43Phe missense_variant 0.13
pepQ 2859466 p.Ala318Gly missense_variant 0.19
thyA 3073780 p.Leu231His missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
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