TB-Profiler result

Run: SRR24114361
Summary

Run ID: SRR24114361

Sample name:

Date: 16-04-2023 21:33:34

Number of reads: 4329851

Percentage reads mapped: 99.73

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.Met434Val (1.00), rpoB p.His445Asn (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (1.00), embB p.Gln497Arg (1.00)
Pyrazinamide R pncA c.391delG (1.00), pncA c.391delG (1.00)
Streptomycin R rrs n.906A>G (1.00), gid c.102delG (1.00)
Fluoroquinolones R gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.77)
Moxifloxacin R gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.77)
Ofloxacin R gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.77)
Levofloxacin R gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.77)
Ciprofloxacin R gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.77)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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 7572 p.Ser91Pro missense_variant 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.77 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761106 p.Met434Val missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.391delG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 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 7350 p.Pro17Thr missense_variant 0.69
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575283 c.-65C>G upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.15
mshA 576113 p.Arg256Gly missense_variant 0.34
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.15
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
embR 1416814 c.534G>A synonymous_variant 1.0
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
PPE35 2170065 p.Ala183Gly missense_variant 0.19
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
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.24
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.37
panD 4044023 c.259C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.2
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