TB-Profiler result

Run: ERR4797097
Summary

Run ID: ERR4797097

Sample name:

Date: 2024-10-04T23:07:53.616428

Number of reads: 5161406

Percentage reads mapped: 99.6

Median coverage: 140.0

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 0.2
lineage2 East-Asian RD105 0.81
lineage1.1 Indo-Oceanic RD239 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage1 Indo-Oceanic RD239 0.2
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Thr76Pro 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 eis c.-12C>T Assoc w R
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 0.76 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Pro missense_variant 0.13 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.78 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289016 p.Thr76Pro missense_variant 0.79 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.74 kanamycin Assoc w R
embB 4247429 p.Met306Val missense_variant 0.83 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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.22 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 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8574 p.Leu425Phe missense_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9047 c.1746C>T synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.2 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
gyrA 9443 c.2142G>A synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.15 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.13 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
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576000 p.Asp218Ala missense_variant 0.26 isoniazid Not assoc w R - Interim
ethionamide Uncertain significance
ccsA 620553 c.663T>C synonymous_variant 0.81 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.81 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.71 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.2 ethionamide
nusG 734020 c.-234A>C upstream_gene_variant 0.84 rifampicin
nusG 734116 c.-138T>C upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.23 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.13 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.86 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.2 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 0.71 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.14 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78 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 0.26 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 0.81 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.18 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.24 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.25 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.33 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 0.29 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 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.2 pyrazinamide Uncertain significance
PPE35 2169369 p.Gly415Ala missense_variant 0.19 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.32 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 0.28 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22 isoniazid
ahpC 2726370 c.179dupT frameshift_variant 0.2 isoniazid Uncertain significance
Rv2681 2996912 c.174C>T synonymous_variant 0.16 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23 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 0.24 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.25 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 0.22 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.74 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640211 c.-332T>G upstream_gene_variant 0.73 pretomanid
delamanid
clofazimine
clpC1 4040517 p.Val63Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.16 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 0.17 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.2 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 0.83 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.16 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.17 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.16 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.87 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.83 ethambutol Not assoc w R
aftB 4268765 c.72T>C synonymous_variant 0.18 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.22 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.11 ethambutol Not assoc w R
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 0.22 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 0.25 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.65 streptomycin Not assoc w R