TB-Profiler result

Run: SRR25827419
Summary

Run ID: SRR25827419

Sample name:

Date: 21-03-2024 07:08:33

Number of reads: 7010348

Percentage reads mapped: 98.77

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 (0.45)
Isoniazid R katG p.Ser315Thr (0.50)
Ethambutol R embA c.-11C>A (0.46)
Pyrazinamide R pncA p.Thr135Pro (0.48)
Streptomycin R rpsL p.Lys88Arg (0.53)
Fluoroquinolones R gyrA p.Asp94Gly (0.52)
Moxifloxacin R gyrA p.Asp94Gly (0.52)
Ofloxacin R gyrA p.Asp94Gly (0.52)
Levofloxacin R gyrA p.Asp94Gly (0.52)
Ciprofloxacin R gyrA p.Asp94Gly (0.52)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.672dupG (0.45), ethA c.672dupG (0.45)
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
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 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.53 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.5 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.48 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.46 ethambutol
ethA 4326801 c.672dupG frameshift_variant 0.45 ethionamide, ethionamide
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 8553 p.Arg418Gly missense_variant 0.45
gyrA 8948 c.1647G>A synonymous_variant 0.52
gyrA 9033 p.Arg578Trp missense_variant 0.44
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575998 c.652dupG frameshift_variant 0.44
mshA 576002 c.656delA frameshift_variant 0.46
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778892 p.Leu5Pro missense_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_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 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.51
pncA 2289365 c.-125delC upstream_gene_variant 0.97
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
Rv2752c 3065935 c.256dupC frameshift_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449672 p.Tyr390Ser missense_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474901 p.Ser299Arg missense_variant 0.47
fbiB 3642877 p.Lys448Arg missense_variant 0.49
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245227 c.1995C>T synonymous_variant 0.52
embB 4247028 p.Leu172Arg missense_variant 0.16
embB 4247702 p.Pro397Ser missense_variant 0.44
embB 4249000 c.2487T>G synonymous_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0