TB-Profiler result

Run: SRR25827749
Summary

Run ID: SRR25827749

Sample name:

Date: 16-03-2024 06:16:03

Number of reads: 8546682

Percentage reads mapped: 98.83

Strain: lineage4;lineage3;lineage2.2.1

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 (0.46), rpoB p.Ile491Phe (0.52)
Isoniazid R fabG1 c.-17G>T (0.56), fabG1 c.-15C>T (0.22), katG p.Ser315Thr (0.95)
Ethambutol R embB p.Met306Val (0.18), embB p.Gln497Arg (0.69)
Pyrazinamide R pncA c.407dupA (0.38), pncA c.407dupA (0.38), pncA p.Gly132Ala (0.24)
Streptomycin R rpsL p.Lys43Arg (0.41), rpsL p.Lys88Arg (0.50), gid c.87delC (0.53)
Fluoroquinolones R gyrA p.Ala90Val (0.18)
Moxifloxacin R gyrA p.Ala90Val (0.18)
Ofloxacin R gyrA p.Ala90Val (0.18)
Levofloxacin R gyrA p.Ala90Val (0.18)
Ciprofloxacin R gyrA p.Ala90Val (0.18)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.56), fabG1 c.-15C>T (0.22)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.56)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.56
lineage2 East-Asian Beijing RD105 0.27
lineage4 Euro-American LAM;T;S;X;H None 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.29
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.27
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 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.46 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.52 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.41 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.5 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.56 linezolid
fabG1 1673423 c.-17G>T upstream_gene_variant 0.56 isoniazid, ethionamide
fabG1 1673425 c.-15C>T upstream_gene_variant 0.22 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2288834 c.407dupA frameshift_variant 0.38 pyrazinamide, pyrazinamide
pncA 2288847 p.Gly132Ala missense_variant 0.24 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.18 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.69 ethambutol
gid 4408115 c.87delC frameshift_variant 0.53 streptomycin
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 7563 p.Gly88Ser missense_variant 0.44
gyrA 7585 p.Ser95Thr missense_variant 0.86
gyrA 8168 p.Glu289Asp missense_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 0.86
fgd1 491290 p.Val170Met missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.9
mshA 575907 p.Ala187Val missense_variant 0.32
ccsA 620625 p.Ile245Met missense_variant 0.26
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.48
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 764669 p.Pro434Thr missense_variant 0.45
rpoC 764840 p.Ile491Val missense_variant 0.29
rpoC 765200 p.Val611Ile missense_variant 0.48
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpR5 779004 c.19delG frameshift_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833612 p.Ala24Gly missense_variant 0.44
rpsA 1834177 c.636A>C synonymous_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2168149 p.Pro822Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.59
pncA 2289365 c.-125delC upstream_gene_variant 0.58
ahpC 2726105 c.-88G>A upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 0.89
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.87
Rv3236c 3612813 p.Thr102Ala missense_variant 0.3
alr 3841473 c.-53G>A upstream_gene_variant 0.51
rpoA 3878637 c.-130G>C upstream_gene_variant 0.17
embC 4240413 p.Leu184Arg missense_variant 0.14
embC 4241022 p.Ala387Val missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 0.52
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.27
ubiA 4269296 p.Met180Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.87
gid 4407620 p.Tyr195His missense_variant 0.21
gid 4407927 p.Glu92Asp missense_variant 0.27