TB-Profiler result

Run: SRR25827484
Summary

Run ID: SRR25827484

Sample name:

Date: 2024-10-04T10:16:10.612754

Number of reads: 10591745

Percentage reads mapped: 98.92

Median coverage: 357.0

Strain: lineage1;lineage2.2.1;lineage3;lineage4

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
lineage3 East-African-Indian RD750 0.12
lineage2 East-Asian RD105 0.63
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.64
lineage2.2 East-Asian (Beijing) RD105;RD207 0.64
lineage4 Euro-American None 0.06
lineage1 Indo-Oceanic RD239 0.18
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
p.Leu27Pro 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
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 0.15 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 0.45 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.16 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 0.9 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.17 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.49 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.17 ethambutol Assoc w R
gid 4408137 p.Tyr22* stop_gained 0.13 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.19 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 0.18 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.22 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.92 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.38 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.58 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.62 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.17 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.15 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.19 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.15 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.21 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.24 rifampicin Uncertain significance
rpoC 767181 p.Ala1271Val missense_variant 0.25 rifampicin
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 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.33 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.13 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65 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 0.16 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.17 ethambutol
embR 1417753 c.-406A>C upstream_gene_variant 0.28 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.62 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.19 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.15 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.93 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 0.22 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.94 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.94 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.18 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 0.16 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.15 isoniazid
folC 2747470 p.Ile43Ala missense_variant 0.22 para-aminosalicylic_acid
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784211 c.-169A>C upstream_gene_variant 0.38 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.95 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.15 ethionamide Uncertain significance
Rv3083 3448936 p.Tyr145Asp missense_variant 0.13 ethionamide Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.25 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.6 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.19 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.91 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.21 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.6 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640457 c.-86G>C upstream_gene_variant 0.29 pretomanid
delamanid
clofazimine Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.14 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.23 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 4138622 c.1134C>T synonymous_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.2 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.17 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.24 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 0.6 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.21 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.19 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.6 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.17 ethambutol Not assoc w R
ethA 4326069 p.Arg469Trp missense_variant 0.32 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.27 ethionamide Uncertain significance
ethA 4326878 p.Ala199Asp missense_variant 0.13 ethionamide
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 0.18 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.94 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.93 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.24 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.6 streptomycin Not assoc w R