TB-Profiler result

Run: SRR25827674
Summary

Run ID: SRR25827674

Sample name:

Date: 16-03-2024 00:34:19

Number of reads: 3877980

Percentage reads mapped: 98.32

Strain: lineage3;lineage2.2.1.1

Drug-resistance: 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 (1.00)
Isoniazid R fabG1 c.-15C>T (0.24), katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.56), embB p.Gln497Arg (0.37)
Pyrazinamide R pncA p.Gly132Ala (0.26), pncA c.-11A>G (0.45)
Streptomycin R rpsL p.Lys43Arg (0.89), rpsL p.Lys88Arg (0.18)
Fluoroquinolones R gyrA p.Asp94Gly (0.80)
Moxifloxacin R gyrA p.Asp94Gly (0.80)
Ofloxacin R gyrA p.Asp94Gly (0.80)
Levofloxacin R gyrA p.Asp94Gly (0.80)
Ciprofloxacin R gyrA p.Asp94Gly (0.80)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.24)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.43)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.15
lineage2 East-Asian Beijing RD105 0.84
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.84
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.58
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 0.8 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.43 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.24 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.26 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.45 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.56 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.37 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.89
ccsA 620625 p.Ile245Met missense_variant 0.9
rpoB 759746 c.-61C>T upstream_gene_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764723 p.Phe452Leu missense_variant 0.5
rpoC 764840 p.Ile491Val missense_variant 0.28
rpoC 767123 p.Val1252Leu missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpR5 779156 p.Leu56Arg missense_variant 0.54
mmpS5 779615 c.-710C>G upstream_gene_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.86
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
pncA 2289047 c.195C>T synonymous_variant 0.23
eis 2714846 p.Val163Ile missense_variant 0.56
folC 2747195 p.Asp135Gly missense_variant 0.51
Rv2752c 3064700 p.Ser498Pro missense_variant 0.15
Rv2752c 3065864 p.Ala110Ser missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473820 c.-187C>A upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.24
whiB7 3568874 c.-195C>T upstream_gene_variant 0.49
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86
alr 3840259 p.Tyr388Asp missense_variant 0.43
embC 4241022 p.Ala387Val missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.38
embA 4243216 c.-17G>A upstream_gene_variant 0.4
embA 4243460 c.228C>T synonymous_variant 0.85
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4248115 c.1602C>T synonymous_variant 0.55
aftB 4267647 p.Asp397Gly missense_variant 0.86
ethA 4326593 p.Cys294Phe missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 0.86