TB-Profiler result

Run: ERR4830354
Summary

Run ID: ERR4830354

Sample name:

Date: 2024-10-04T00:04:08.823226

Number of reads: 3729442

Percentage reads mapped: 99.05

Median coverage: 90.0

Strain: lineage1.1.1;lineage4.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.71
lineage4.2 Euro-American None 0.7
lineage1.1 Indo-Oceanic RD239 0.26
lineage4 Euro-American None 0.75
lineage1 Indo-Oceanic RD239 0.29
lineage1.1.1 Indo-Oceanic RD239 0.28
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.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.77 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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 5627 p.Ala130Ser missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.28 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 0.35 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.26 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.35 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.31 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.23 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.22 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.3 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.44 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.31 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 0.21 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
rpsL 781694 c.135G>A synonymous_variant 0.24 streptomycin Not assoc w R - Interim
rplC 800204 c.-605T>C upstream_gene_variant 0.76 linezolid
rplC 800349 c.-460C>G upstream_gene_variant 0.19 linezolid Uncertain significance
rplC 800357 c.-452C>A upstream_gene_variant 0.18 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 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 0.26 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.26 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 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.21 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.33 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.22 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
bacA 2063106 c.1623G>A synonymous_variant 0.36 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063685 c.1044G>A synonymous_variant 0.79 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.64 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.38 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.35 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223144 p.Arg7Ser missense_variant 0.28 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223758 c.-594A>G upstream_gene_variant 0.73 bedaquiline
clofazimine
kasA 2518132 c.18C>T synonymous_variant 0.12 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.38 isoniazid
ahpC 2726763 p.Leu191Phe missense_variant 0.3 isoniazid Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.19 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
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.74 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.73 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.73 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.21 ethionamide Uncertain significance
Rv3236c 3612469 c.648A>G synonymous_variant 0.71 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
mtrA 3627665 c.-316C>A upstream_gene_variant 0.37 rifampicin Uncertain significance
bedaquiline
rpoA 3878630 c.-124delC upstream_gene_variant 0.27 rifampicin Not assoc w R
clpC1 4038545 c.2160C>T synonymous_variant 0.28 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.27 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 0.4 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.23 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 0.31 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.19 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.26 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.17 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.25 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.2 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.3 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 0.28 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 0.29 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.35 streptomycin Not assoc w R