TB-Profiler result

Run: SRR25827455
Summary

Run ID: SRR25827455

Sample name:

Date: 2024-10-04T18:38:35.646191

Number of reads: 10252735

Percentage reads mapped: 98.57

Median coverage: 342.0

Strain: lineage1.1.2;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
lineage1.1.2 Indo-Oceanic RD239 0.54
lineage2 East-Asian RD105 0.46
lineage1.1 Indo-Oceanic RD239 0.55
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.45
lineage2.2 East-Asian (Beijing) RD105;RD207 0.46
lineage1 Indo-Oceanic RD239 0.54
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Leu27Pro 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
capreomycin
kanamycin
cycloserine
ethionamide
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 0.38 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.52 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.46 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.55 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
gyrB 6112 p.Met291Ile missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.55 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 8452 p.Ala384Val missense_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.58 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 13298 p.Ile87Met missense_variant 0.59 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.42 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.42 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.5 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.53 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.54 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.54 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.58 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.56 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.56 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.42 rifampicin Uncertain significance
rpoC 767181 p.Ala1271Val missense_variant 0.48 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.49 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43 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 0.56 linezolid 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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.43 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.56 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.49 ethambutol
embR 1417753 c.-406A>C upstream_gene_variant 0.44 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.54 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.49 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.56 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.56 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 0.52 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.53 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.54 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
Rv1979c 2223767 c.-604_-603delGAinsCT upstream_gene_variant 0.48 bedaquiline
clofazimine
kasA 2518132 c.18C>T synonymous_variant 0.58 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.54 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.59 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.55 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 0.56 ethionamide Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.39 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.49 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.54 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 3626467 c.147G>A synonymous_variant 0.53 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.47 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640457 c.-86G>C upstream_gene_variant 0.48 pretomanid
delamanid
clofazimine Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.53 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.52 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.61 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
embC 4240671 p.Thr270Ile missense_variant 0.53 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.54 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 0.43 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.56 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.56 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.14 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.5 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.55 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.41 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.56 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.54 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.55 ethambutol Not assoc w R
ethA 4326069 p.Arg469Trp missense_variant 0.45 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.39 ethionamide 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 0.51 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 0.49 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.45 streptomycin Not assoc w R
gid 4408093 p.Gly37Val missense_variant 0.54 streptomycin Uncertain significance