TB-Profiler result

Run: ERR1035091
Summary

Run ID: ERR1035091

Sample name:

Date: 2024-10-04T20:14:30.951608

Number of reads: 4789271

Percentage reads mapped: 99.34

Median coverage: 89.0

Strain: lineage1.1.1;lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.38
lineage4 Euro-American None 0.65
lineage4.8 Euro-American (mainly T) RD219 0.66
lineage1 Indo-Oceanic RD239 0.33
lineage1.1.1 Indo-Oceanic RD239 0.32
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
gid 4408087 c.115delC frameshift_variant 0.38 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 0.4 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 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13158 p.Gly134Asp missense_variant 0.45 isoniazid Uncertain significance
Rv0010c 13275 p.Tyr95Cys missense_variant 0.45 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.47 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.36 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.33 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.42 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.39 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.26 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.39 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 0.34 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777804 p.Ile226Thr missense_variant 0.25 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 0.28 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.41 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.36 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.36 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.23 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.45 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.33 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.37 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.35 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 0.33 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.27 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102809 p.Lys78Asn missense_variant 0.65 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.3 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.41 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.39 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.42 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
pncA 2289414 c.-173A>G upstream_gene_variant 0.6 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.32 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.34 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.6 capreomycin
Rv2681 2996984 c.246C>A synonymous_variant 0.62 capreomycin
Rv2752c 3064632 c.1560C>T synonymous_variant 0.41 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 0.35 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623744 p.Asp389Glu missense_variant 0.26 rifampicin
bedaquiline
lpqB 3624486 p.Asp142Gly missense_variant 0.28 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.39 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641064 c.522G>A synonymous_variant 0.41 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840280 p.Asp381Asn missense_variant 0.36 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.38 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.44 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 4138537 p.Asp407Asn missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.32 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.32 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.3 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.24 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.37 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.33 ethambutol Not assoc w R
aftB 4268051 c.786G>A synonymous_variant 0.4 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.32 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.32 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338400 p.Trp41Leu missense_variant 0.59 kanamycin
capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 0.61 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.4 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338605 c.-84C>G upstream_gene_variant 0.61 kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.38 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.46 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.41 streptomycin Not assoc w R