TB-Profiler result

Run: SRR25827402

Summary

Run ID: SRR25827402

Sample name:

Date: 01-02-2024 09:46:40

Number of reads: 7437987

Percentage reads mapped: 99.17

Strain: lineage4.8;lineage3.1.2;lineage2.2.1;lineage1.1.2

Drug-resistance: 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 (0.79)
Isoniazid R fabG1 c.-15C>T (0.22), katG p.Ser315Thr (0.71)
Ethambutol R embB p.Met306Val (0.40), embB p.Gln497Arg (0.20)
Pyrazinamide R pncA p.Gly132Ala (0.25), pncA p.Asp63Gly (0.13)
Streptomycin R rpsL p.Lys43Arg (0.53)
Fluoroquinolones R gyrA p.Gly88Ala (0.19), gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.14)
Moxifloxacin R gyrA p.Gly88Ala (0.19), gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.14)
Ofloxacin R gyrA p.Gly88Ala (0.19), gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.14)
Levofloxacin R gyrA p.Gly88Ala (0.19), gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.14)
Ciprofloxacin R gyrA p.Gly88Ala (0.19), gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.14)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-37G>T (0.14)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.22)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.21)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.31
lineage2 East-Asian Beijing RD105 0.4
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage1 Indo-Oceanic EAI RD239 0.12
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.09
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.41
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.13
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.3
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.1
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.28
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.39
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 7564 p.Gly88Ala missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.79 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.53 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.21 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.22 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.25 pyrazinamide
pncA 2289054 p.Asp63Gly missense_variant 0.13 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.14 kanamycin
embB 4247429 p.Met306Val missense_variant 0.4 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.2 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
gyrB 6112 p.Met291Ile missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.86
gyrA 8168 p.Glu289Asp missense_variant 0.15
gyrA 8348 c.1047C>T synonymous_variant 0.24
gyrA 8557 p.Ala419Asp missense_variant 0.23
gyrA 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491290 p.Val170Met missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 0.85
mshA 575907 p.Ala187Val missense_variant 0.44
ccsA 620625 p.Ile245Met missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 764363 p.Gly332Ser missense_variant 0.13
rpoC 764817 p.Val483Ala missense_variant 0.16
rpoC 764840 p.Ile491Val missense_variant 0.23
rpoC 765862 p.Phe831Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776182 p.Asp767Asn missense_variant 0.46
mmpS5 779615 c.-710C>G upstream_gene_variant 0.42
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801267 c.459A>G synonymous_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673406 c.-796C>G upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2168149 p.Pro822Ser missense_variant 0.14
PPE35 2168349 p.Gly755Ala missense_variant 0.27
PPE35 2168604 p.Pro670Leu missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.35
pncA 2289365 c.-125delC upstream_gene_variant 0.3
kasA 2518132 c.18C>T synonymous_variant 0.14
kasA 2519304 p.Ala397Val missense_variant 0.26
ahpC 2726105 c.-88G>A upstream_gene_variant 0.32
Rv2752c 3065773 p.Glu140Gly missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.88
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
clpC1 4039729 p.Asp326Asn missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.14
embC 4241022 p.Ala387Val missense_variant 0.22
embC 4241042 p.Asn394Asp missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.42
embA 4243848 p.Val206Met missense_variant 0.15
embA 4245417 p.Gly729Arg missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 0.19
embB 4247028 p.Leu172Arg missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 0.12
embB 4249485 p.Gly991Val missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.44
ubiA 4269296 p.Met180Val missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.82
gid 4407620 p.Tyr195His missense_variant 0.26
gid 4407927 p.Glu92Asp missense_variant 0.38