TB-Profiler result

Run: SRR25827328
Summary

Run ID: SRR25827328

Sample name:

Date: 21-03-2024 03:34:40

Number of reads: 6607361

Percentage reads mapped: 99.17

Strain: lineage2.2.1.2

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 (0.99)
Isoniazid R fabG1 c.-15C>T (0.52), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (0.44), embB p.Gln497Arg (1.00)
Pyrazinamide R pncA p.Gly132Ala (0.55), pncA p.Phe94Leu (0.46)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Val670Phe (0.54), gyrA p.Asp94Gly (0.48)
Moxifloxacin R gyrB p.Val670Phe (0.54), gyrA p.Asp94Gly (0.48)
Ofloxacin R gyrB p.Val670Phe (0.54), gyrA p.Asp94Gly (0.48)
Levofloxacin R gyrB p.Val670Phe (0.54), gyrA p.Asp94Gly (0.48)
Ciprofloxacin R gyrB p.Val670Phe (0.54), gyrA p.Asp94Gly (0.48)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.52)
Clofazimine
Para-aminosalicylic_acid R folC p.Ser150Gly (0.47)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 0.48
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
gyrB 7247 p.Val670Phe missense_variant 0.54 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.52 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.55 pyrazinamide
pncA 2288962 p.Phe94Leu missense_variant 0.46 pyrazinamide
folC 2747151 p.Ser150Gly missense_variant 0.47 para-aminosalicylic_acid
embA 4243221 c.-12C>T upstream_gene_variant 0.44 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 491290 p.Val170Met missense_variant 0.47
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576508 c.1161C>A synonymous_variant 0.43
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Ala missense_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407031 c.310C>T synonymous_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064843 p.Asp450Gly missense_variant 0.53
Rv2752c 3065453 p.Gln247* stop_gained 0.45
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.6
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.52
embC 4242039 p.Ala726Gly missense_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327103 p.Gly124Val missense_variant 0.51
whiB6 4338404 p.Arg40Cys missense_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.52
gid 4407927 p.Glu92Asp missense_variant 1.0