TB-Profiler result

Run: SRR25827524

Summary

Run ID: SRR25827524

Sample name:

Date: 02-02-2024 08:17:55

Number of reads: 8611834

Percentage reads mapped: 99.14

Strain: lineage4;lineage2.2.1.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.91)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.65)
Pyrazinamide R pncA p.Thr177Pro (0.40), pncA p.Leu27Pro (0.20)
Streptomycin R rpsL p.Lys43Arg (0.68)
Fluoroquinolones R gyrA p.Asp94Ala (0.49)
Moxifloxacin R gyrA p.Asp94Ala (0.49)
Ofloxacin R gyrA p.Asp94Ala (0.49)
Levofloxacin R gyrA p.Asp94Ala (0.49)
Ciprofloxacin R gyrA p.Asp94Ala (0.49)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.693dupG (0.37), ethA c.693dupG (0.37)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.45)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.78
lineage4 Euro-American LAM;T;S;X;H None 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.79
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.15
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.Asp94Ala missense_variant 0.49 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.4 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.2 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.45 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.65 ethambutol
ethA 4326780 c.693dupG frameshift_variant 0.37 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.88
mshA 575907 p.Ala187Val missense_variant 0.6
ccsA 620625 p.Ile245Met missense_variant 0.75
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 764840 p.Ile491Val missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.66
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.82
rrs 1471659 n.-187C>T upstream_gene_variant 0.97
rpsA 1833585 p.Asp15Gly missense_variant 0.39
rpsA 1834177 c.636A>C synonymous_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.16
thyA 3073868 p.Thr202Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77
embC 4241022 p.Ala387Val missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.78
embB 4247028 p.Leu172Arg missense_variant 0.24
embB 4247861 p.Ile450Leu missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 0.82
ethA 4326676 p.Ser266Arg missense_variant 0.13
ethA 4327472 c.2T>C start_lost 0.12
whiB6 4338233 p.Ser97Pro missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407620 p.Tyr195His missense_variant 0.41
gid 4407927 p.Glu92Asp missense_variant 0.8