TB-Profiler result

Run: ERR227993
Summary

Run ID: ERR227993

Sample name:

Date: 2024-10-05T07:06:12.292985

Number of reads: 4492309

Percentage reads mapped: 99.55

Median coverage: 99.0

Strain: lineage2.2.1;lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.71
lineage4.2 Euro-American None 0.28
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.69
lineage2.2 East-Asian (Beijing) RD105;RD207 0.69
lineage4 Euro-American None 0.31
lineage4.2.1 Euro-American (TUR) None 0.28
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
p.Glu761Asp Uncertain significance Mutation from literature
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.Asp354Ala Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Val180Gly Assoc w R
p.Val155Met Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
c.-15C>G Uncertain significance Mutation from literature
c.-37G>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1427_1428dupAG Assoc w R
c.-7T>C Assoc w R - Interim
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.44 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.18 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.23 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.47 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.26 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288703 p.Val180Gly missense_variant 0.22 pyrazinamide Assoc w R
pncA 2288779 p.Val155Met missense_variant 0.24 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.24 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
eis 2715347 c.-15C>G upstream_gene_variant 0.29 kanamycin Uncertain significance Mutation from literature
eis 2715369 c.-37G>T upstream_gene_variant 0.57 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.57 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.36 ethambutol Assoc w R
ethA 4326045 c.1427_1428dupAG frameshift_variant 0.23 ethionamide Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.58 ethionamide Assoc w R - Interim
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.35 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.69 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575182 c.-166A>G upstream_gene_variant 0.33 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.69 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.65 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.69 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.62 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.79 rifampicin Not assoc w R
rpoC 764703 p.Lys445Arg missense_variant 0.14 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.54 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.75 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.74 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.66 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.28 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.49 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.72 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.25 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.23 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.73 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.18 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289226 p.Ile6Leu missense_variant 0.61 pyrazinamide Not assoc w R - Interim
ald 3086731 c.-89A>G upstream_gene_variant 0.2 cycloserine
ald 3086742 c.-78A>C upstream_gene_variant 0.22 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3449264 p.Leu254Pro missense_variant 0.23 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.66 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.71 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877960 p.Val183Gly missense_variant 0.28 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.7 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.38 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.75 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.32 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.23 ethionamide
whiB6 4338371 p.Thr51Pro missense_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.59 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.71 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R