TB-Profiler result

Run: SRR25827429
Summary

Run ID: SRR25827429

Sample name:

Date: 2024-04-15T13:26:01.907390

Number of reads: 3407230

Percentage reads mapped: 98.62

Median coverage: 108.0

Strain: lineage1.1.2;lineage2.2.1;lineage4.9

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
lineage1.1.2 Indo-Oceanic RD239 0.45
lineage2 East-Asian RD105 0.36
lineage1.1 Indo-Oceanic RD239 0.44
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.34
lineage2.2 East-Asian (Beijing) RD105;RD207 0.32
lineage4 Euro-American None 0.15
lineage1 Indo-Oceanic RD239 0.46
lineage4.9 Euro-American (H37Rv-like) None 0.07
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)
c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg 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 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
c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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 7570 p.Ala90Val missense_variant 0.2 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.3 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.28 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.15 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 1673432 c.-770T>C upstream_gene_variant 0.13 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.5 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.13 pyrazinamide 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 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.4 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.24 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.15 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 0.37 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.38 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.3 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.37 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.43 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.6 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.48 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.38 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.14 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.24 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.46 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.95 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.33 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.44 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.96 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.42 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.93 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.39 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.47 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.58 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.86 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673761 p.Val108Ile missense_variant 0.35 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.48 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.4 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.97 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.88 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.47 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101955 p.Gln363Ser missense_variant 0.41 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.86 isoniazid Not assoc w R
PPE35 2167701 p.Ala971Gly missense_variant 0.41 pyrazinamide Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.43 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.39 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.34 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.31 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.43 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.5 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
Rv2752c 3064896 c.1296T>C synonymous_variant 0.45 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.94 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.34 ethionamide Uncertain significance
whiB7 3568425 c.255T>G synonymous_variant 0.15 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.39 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.43 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.29 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.52 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.39 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.42 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 0.52 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.48 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.9 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.33 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.49 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.47 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.46 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.47 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.48 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.42 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.41 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.91 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.43 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.94 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.76 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.16 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.51 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.31 streptomycin Not assoc w R