TB-Profiler result

Run: ERR270671
Summary

Run ID: ERR270671

Sample name:

Date: 2024-10-05T08:29:18.856860

Number of reads: 4560406

Percentage reads mapped: 99.24

Median coverage: 109.0

Strain: lineage1.1.3.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.92
lineage1.1.3.2 Indo-Oceanic RD239 0.91
lineage1.1 Indo-Oceanic RD239 0.93
lineage1 Indo-Oceanic RD239 0.93
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1054delG 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
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid Assoc w R High-level resistance
ethA 4326419 c.1054delG frameshift_variant 0.94 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 0.96 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 8188 p.Leu296Pro missense_variant 0.95 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.91 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.87 isoniazid Not assoc w R
Rv0010c 13564 c.-6G>A upstream_gene_variant 0.89 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619695 c.-196G>A upstream_gene_variant 0.84 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.83 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.9 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 761483 c.1677G>A synonymous_variant 0.89 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.12 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 0.95 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.95 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.94 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.94 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.81 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
Rv1129c 1254743 c.-209C>T upstream_gene_variant 0.91 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417267 c.80dupC frameshift_variant 0.89 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.97 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.9 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.91 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.97 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 0.93 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064420 c.309C>T synonymous_variant 0.92 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.9 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.17 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.91 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.93 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.15 isoniazid Not assoc w R
ahpC 2726515 p.Phe108Ser missense_variant 0.89 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.92 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 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.9 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642173 c.639G>A synonymous_variant 0.9 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoA 3878687 c.-180A>C upstream_gene_variant 0.92 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.95 pyrazinamide Not assoc w R - Interim
panD 4045160 c.-879G>A upstream_gene_variant 0.89 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.93 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 0.95 ethambutol Not assoc w R
embC 4240807 c.945C>T synonymous_variant 0.93 ethambutol Not assoc w R - Interim
embC 4241042 p.Asn394Asp missense_variant 0.98 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243701 p.Gly157Cys missense_variant 0.89 ethambutol
embA 4243848 p.Val206Met missense_variant 0.97 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.93 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248781 c.2268G>A synonymous_variant 0.88 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.9 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.92 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 0.89 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.93 streptomycin Not assoc w R - Interim
gid 4407792 c.411G>C synonymous_variant 0.91 streptomycin
gid 4407873 c.330G>T synonymous_variant 0.94 streptomycin Not assoc w R
gid 4407973 p.Val77Gly missense_variant 0.9 streptomycin Uncertain significance