TB-Profiler result

Run: SRR25827558
Summary

Run ID: SRR25827558

Sample name:

Date: 02-02-2024 10:07:34

Number of reads: 9251991

Percentage reads mapped: 99.02

Strain: lineage3;lineage2.2.1.2;lineage2.2.1.1

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.Ser450Trp (0.29), rpoB p.Ser450Leu (0.61)
Isoniazid R katG p.Ile317Val (0.13), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.70)
Pyrazinamide R pncA p.Leu27Pro (0.16)
Streptomycin R rpsL p.Lys43Arg (0.74)
Fluoroquinolones R gyrA p.Ala90Val (0.17), gyrA p.Asp94Gly (0.41)
Moxifloxacin R gyrA p.Ala90Val (0.17), gyrA p.Asp94Gly (0.41)
Ofloxacin R gyrA p.Ala90Val (0.17), gyrA p.Asp94Gly (0.41)
Levofloxacin R gyrA p.Ala90Val (0.17), gyrA p.Asp94Gly (0.41)
Ciprofloxacin R gyrA p.Ala90Val (0.17), gyrA p.Asp94Gly (0.41)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Trp240* (0.24)
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 0.11
lineage2 East-Asian Beijing RD105 0.83
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.83
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.82
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.2
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 0.07
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 7570 p.Ala90Val missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.29 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.61 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.74 streptomycin
katG 2155163 p.Ile317Val missense_variant 0.13 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.16 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol
ethA 4326755 p.Trp240* stop_gained 0.24 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 0.97
mshA 575907 p.Ala187Val missense_variant 0.6
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoB 759746 c.-61C>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776182 p.Asp767Asn missense_variant 0.69
mmpR5 779371 c.386dupC frameshift_variant 0.17
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 0.91
rpsA 1834177 c.636A>C synonymous_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289027 p.Cys72Phe missense_variant 0.27
pncA 2289047 c.195C>T synonymous_variant 0.17
eis 2714846 p.Val163Ile missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.84
rpoA 3877960 p.Val183Gly missense_variant 0.18
embC 4241022 p.Ala387Val missense_variant 0.37
embC 4242075 p.Arg738Gln missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.84
embB 4248115 c.1602C>T synonymous_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 0.8
ethA 4326676 p.Ser266Arg missense_variant 0.23
ethA 4327472 c.2T>C start_lost 0.16
whiB6 4338233 p.Ser97Pro missense_variant 0.17
whiB6 4338365 p.Cys53Gly missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407620 p.Tyr195His missense_variant 0.28
gid 4407927 p.Glu92Asp missense_variant 0.8