TB-Profiler result

Run: SRR11662693
Summary

Run ID: SRR11662693

Sample name:

Date: 2024-10-04T13:20:31.741845

Number of reads: 8378206

Percentage reads mapped: 99.08

Median coverage: 246.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.25
lineage1.1 Indo-Oceanic RD239 0.75
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.25
lineage2.2 East-Asian (Beijing) RD105;RD207 0.28
lineage1 Indo-Oceanic RD239 0.74
lineage1.1.1 Indo-Oceanic RD239 0.71
lineage1.1.1.1 Indo-Oceanic RD239 0.76
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val 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)
p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Asp328Gly Uncertain significance Mutation from literature
p.Gly406Ala Assoc w R
pyrazinamide pncA c.391dupG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ser94Ala 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
gyrA 7582 p.Asp94Gly missense_variant 0.33 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.29 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.23 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.19 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)
inhA 1674481 p.Ser94Ala missense_variant 0.28 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
pncA 2288850 c.391dupG frameshift_variant 0.26 pyrazinamide Assoc w R
embB 4247496 p.Asp328Gly missense_variant 0.25 ethambutol Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.23 ethambutol 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
dnaA 714 c.714C>T synonymous_variant 0.72 isoniazid
gyrB 6112 p.Met291Ile missense_variant 0.74 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7905 p.Phe202Leu missense_variant 0.73 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.73 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
Rv0010c 13275 p.Tyr95Cys missense_variant 0.7 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.72 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.77 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.73 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.74 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.27 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.24 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.23 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.71 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.73 rifampicin Not assoc w R
rpoB 759549 c.-258G>A upstream_gene_variant 0.76 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.74 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.73 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.28 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777212 c.1269C>T synonymous_variant 0.73 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.7 linezolid Not assoc w R
Rv1129c 1254144 p.Thr131Pro missense_variant 0.24 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.76 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.73 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.7 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.75 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.75 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473436 n.-222T>G upstream_gene_variant 0.78 capreomycin
linezolid
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.7 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.77 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.81 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.75 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.67 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155612 p.Phe167Cys missense_variant 0.2 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.71 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.72 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.75 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.73 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.75 ethionamide Uncertain significance
whiB7 3568472 p.Ile70Val missense_variant 0.23 kanamycin
amikacin
streptomycin
whiB7 3568734 c.-55G>A upstream_gene_variant 0.29 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.72 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.27 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877691 p.Gly273Ser missense_variant 0.76 rifampicin Uncertain significance
rpoA 3878630 c.-124delC upstream_gene_variant 0.77 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.72 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138509 p.Ser416Phe missense_variant 0.76 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.76 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.69 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 0.21 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.77 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.78 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.71 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
aftB 4267400 c.1437G>A synonymous_variant 0.72 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.27 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.75 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.79 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338590 c.-69A>C upstream_gene_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
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 4338603 c.-82C>T upstream_gene_variant 0.68 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 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.71 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.23 streptomycin Not assoc w R