TB-Profiler result

Run: ERR234635
Summary

Run ID: ERR234635

Sample name:

Date: 2024-10-05T00:21:55.709592

Number of reads: 4726734

Percentage reads mapped: 99.36

Median coverage: 105.0

Strain: lineage1.1.1.1;lineage4.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.15
lineage1.1 Indo-Oceanic RD239 0.76
lineage4 Euro-American None 0.18
lineage1 Indo-Oceanic RD239 0.77
lineage1.1.1 Indo-Oceanic RD239 0.78
lineage1.1.1.1 Indo-Oceanic RD239 0.74
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-770T>G Assoc w R - Interim Alias fabG1_c.-8T>G. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>G Assoc w R - Interim Alias fabG1_c.-8T>G
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
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin Assoc w R
inhA 1673432 c.-770T>G upstream_gene_variant 0.15 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>G
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>G. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.19 isoniazid Assoc w R High-level resistance
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 5949 p.Ala237Val missense_variant 0.79 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.75 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 7634 c.333C>T synonymous_variant 0.73 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8452 p.Ala384Val missense_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.76 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 13275 p.Tyr95Cys missense_variant 0.76 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.78 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.76 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.66 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.77 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.16 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.74 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.79 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.75 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.84 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 0.84 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777027 p.Thr485Asn missense_variant 0.79 bedaquiline
clofazimine
mmpL5 777310 p.Gly391Ser missense_variant 0.14 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777581 p.Tyr300* stop_gained 0.77 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.12 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.77 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.8 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 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 0.78 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.66 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.81 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.75 pyrazinamide Uncertain significance
rpsA 1834772 p.Arg411Ser missense_variant 0.15 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.75 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.77 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 0.81 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 0.8 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 0.84 isoniazid Not assoc w R
katG 2156389 c.-278G>C upstream_gene_variant 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.78 pyrazinamide Uncertain significance
PPE35 2168435 c.2178C>T synonymous_variant 0.17 pyrazinamide
PPE35 2168703 p.Gly637Asp missense_variant 0.84 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.81 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 0.69 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.71 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.77 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 0.73 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.76 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3626909 c.441C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
alr 3841505 c.-85C>T upstream_gene_variant 0.19 cycloserine
rpoA 3878630 c.-124delC upstream_gene_variant 0.64 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.78 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.8 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 4139074 p.Leu228Val missense_variant 0.74 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.75 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.81 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.2 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.73 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.84 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.79 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.82 ethambutol Not assoc w R
embB 4247825 p.Ala438Thr missense_variant 0.78 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.22 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.74 ethambutol Not assoc w R
ethA 4326446 p.Gly343Ala missense_variant 0.14 ethionamide Uncertain significance
ethR 4328005 p.Ile153Val missense_variant 0.82 ethionamide Uncertain significance
ethA 4328299 c.-826A>G upstream_gene_variant 0.1 ethionamide
whiB6 4338242 p.Gln94Glu missense_variant 0.84 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 0.74 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 0.86 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.79 streptomycin Not assoc w R