TB-Profiler result

Run: SRR25827768
Summary

Run ID: SRR25827768

Sample name:

Date: 2024-04-16T01:51:11.821542

Number of reads: 7131413

Percentage reads mapped: 99.08

Median coverage: 241.0

Strain: lineage1.1.2;lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.1
lineage2 East-Asian RD105 0.72
lineage1.1 Indo-Oceanic RD239 0.11
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.7
lineage2.2 East-Asian (Beijing) RD105;RD207 0.72
lineage4 Euro-American None 0.11
lineage1 Indo-Oceanic RD239 0.12
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
c.174dupC Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Tyr22* Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 Confidence Comment
gyrA 7570 p.Ala90Val missense_variant 0.13 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Gly missense_variant 0.53 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.13 linezolid Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.22 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.2 pyrazinamide Assoc w R
pncA 2289067 c.174dupC frameshift_variant 0.29 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.14 ethambutol Assoc w R
gid 4408137 p.Tyr22* stop_gained 0.17 streptomycin Assoc w R
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 Drugs Confidence
gyrB 6112 p.Met291Ile missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.17 isoniazid Not assoc w R
Rv0010c 13631 c.-73T>C upstream_gene_variant 0.29 isoniazid Uncertain significance
fgd1 491290 p.Val170Met missense_variant 0.25 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.91 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.64 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576456 p.Val370Gly missense_variant 0.16 ethionamide
isoniazid
ccsA 620553 c.663T>C synonymous_variant 0.43 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.69 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.16 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.7 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.15 ethionamide
nusG 734658 c.405A>G synonymous_variant 0.12 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.13 rifampicin Not assoc w R
rpoB 761510 c.1704T>G synonymous_variant 0.14 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.17 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.19 rifampicin Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 0.49 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.22 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.15 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.92 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.71 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.12 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801267 c.459A>G synonymous_variant 0.13 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.87 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254591 c.-57C>T upstream_gene_variant 0.14 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.65 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.17 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.18 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.75 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.85 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102791 c.252A>C synonymous_variant 0.18 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.89 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.14 pyrazinamide Uncertain significance
PPE35 2170785 c.-173T>C upstream_gene_variant 0.13 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.15 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
ald 3086821 p.Met1? start_lost 0.14 cycloserine
Rv3083 3448936 p.Tyr145Asp missense_variant 0.14 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.87 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.68 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.42 clofazimine
pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.14 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.12 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.18 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.17 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.64 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.2 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.24 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.22 ethambutol Not assoc w R
embB 4249485 p.Gly991Val missense_variant 0.17 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.41 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.63 ethambutol Not assoc w R
aftB 4268753 c.84T>G synonymous_variant 0.14 ethambutol Not assoc w R - Interim
ubiA 4269102 c.732C>T synonymous_variant 0.19 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.88 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.89 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.17 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.18 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R