TB-Profiler result

Run: ERR4797643

Summary

Run ID: ERR4797643

Sample name:

Date: 2024-03-25T20:44:51.886187

Number of reads: 3809493

Percentage reads mapped: 99.65

Median coverage: 111.0

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 0.11
lineage2 East-Asian RD105 0.9
lineage1.1 Indo-Oceanic RD239 0.12
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.87
lineage2.2 East-Asian (Beijing) RD105;RD207 0.84
lineage1 Indo-Oceanic RD239 0.12
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn 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.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 ethA p.Trp391* Assoc w R
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 0.89 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asn missense_variant 0.14 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.87 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.9 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.88 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.91 ethambutol Assoc w R
ethA 4326302 p.Trp391* stop_gained 0.8 ethionamide 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 0.15 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 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9047 c.1746C>T synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.12 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 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.14 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.12 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576000 p.Asp218Ala missense_variant 0.18 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.88 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.88 ethionamide Uncertain significance
rpoB 759546 c.-261A>G upstream_gene_variant 0.12 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.14 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763378 c.9C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.14 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.12 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.83 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.16 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.13 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.9 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.11 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.89 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.15 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.2 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
katG 2154549 c.1563G>C synonymous_variant 0.1 isoniazid Not assoc w R - Interim
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
Rv2477c 2784139 c.-98delC upstream_gene_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3064632 c.1560C>T synonymous_variant 0.19 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449623 p.Lys374Glu missense_variant 0.13 ethionamide Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.92 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.18 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.81 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.15 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.1 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 4241042 p.Asn394Asp missense_variant 0.14 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 0.89 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.15 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.1 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.88 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.1 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.91 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.88 streptomycin Not assoc w R