TB-Profiler result

Run: ERR4830347
Summary

Run ID: ERR4830347

Sample name:

Date: 2024-04-15T07:02:25.487093

Number of reads: 6446465

Percentage reads mapped: 96.97

Median coverage: 142.5

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.23
lineage1.1 Indo-Oceanic RD239 0.77
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.22
lineage1 Indo-Oceanic RD239 0.75
lineage1.1.1 Indo-Oceanic RD239 0.74
lineage1.1.1.1 Indo-Oceanic RD239 0.68
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 gid c.471delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ser447Phe Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ser447Phe Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1034delA 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
gyrB 6579 p.Ser447Phe missense_variant 0.14 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid Assoc w R High-level resistance
ethA 4326439 c.1034delA frameshift_variant 0.12 ethionamide Assoc w R
gid 4407731 c.471delG frameshift_variant 0.76 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 0.75 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 7466 c.165G>A synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.72 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 0.73 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.88 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.72 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.73 isoniazid Not assoc w R
Rv0010c 13726 c.-168G>C upstream_gene_variant 0.19 isoniazid
fgd1 490972 p.Arg64Ser missense_variant 0.66 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.31 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.72 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.77 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 0.77 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.76 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.78 rifampicin Not assoc w R
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 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777581 p.Tyr300* stop_gained 0.68 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26 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 0.75 linezolid Not assoc w R
Rv1129c 1254532 p.Met1? start_lost 0.13 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.76 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid 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 0.22 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.78 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.72 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.78 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.72 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.83 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.79 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 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.74 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin 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 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.73 pyrazinamide Uncertain significance
PPE35 2170829 c.-217T>C upstream_gene_variant 0.2 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.77 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.78 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.82 isoniazid
ribD 2986925 c.87C>A synonymous_variant 0.11 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.79 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
thyA 3073768 p.Arg235Gln missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.69 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
Rv3236c 3613786 c.-670G>C upstream_gene_variant 0.23 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.21 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878630 c.-124delC upstream_gene_variant 0.67 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.72 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
glpK 4139074 p.Leu228Val missense_variant 0.76 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240411 c.549G>T synonymous_variant 0.74 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.79 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.77 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 0.2 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.81 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.76 ethambutol Not assoc w R
embA 4244837 c.1605G>C synonymous_variant 0.11 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.77 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
embB 4248195 p.Lys561Arg missense_variant 0.7 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.72 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.85 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.26 ethionamide Uncertain significance
whiB6 4338242 p.Gln94Glu missense_variant 0.76 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4338603 c.-82C>T upstream_gene_variant 0.73 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 4407870 c.333C>G synonymous_variant 0.13 streptomycin
gid 4407873 c.330G>T synonymous_variant 0.79 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.26 streptomycin Not assoc w R