TB-Profiler result

Run: ERR3335730

Summary

Run ID: ERR3335730

Sample name:

Date: 2024-04-14T07:15:35.511678

Number of reads: 6599440

Percentage reads mapped: 99.23

Median coverage: 181.0

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: HR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.91
lineage1.2.2.2 Indo-Oceanic RD239 0.92
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.06
lineage1 Indo-Oceanic RD239 0.92
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.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.14 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.18 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid Assoc w R High-level resistance
gid 4408087 c.115delC frameshift_variant 0.87 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 5075 c.-165C>T upstream_gene_variant 0.89 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.91 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 8452 p.Ala384Val missense_variant 0.89 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.89 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.9 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.89 isoniazid Not assoc w R
Rv0010c 13548 p.Thr4Ile missense_variant 0.94 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.91 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.99 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.92 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.88 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 0.89 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.89 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.94 linezolid 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
Rv1129c 1254747 c.-213C>A upstream_gene_variant 0.91 moxifloxacin
levofloxacin
rifampicin
isoniazid
embR 1417019 p.Cys110Tyr missense_variant 0.93 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.89 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.92 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.92 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 0.99 capreomycin Not assoc w R
tlyA 1918677 c.738G>A synonymous_variant 0.9 capreomycin Not assoc w R - Interim
bacA 2062922 p.Ile603Val missense_variant 0.93 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 2168742 p.Gly624Asp missense_variant 0.93 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.89 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.93 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.9 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.94 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.94 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
rpoA 3878817 c.-310T>A upstream_gene_variant 0.91 rifampicin Not assoc w R
clpC1 4040297 c.408G>A synonymous_variant 0.91 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.93 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.9 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
embC 4240671 p.Thr270Ile missense_variant 0.92 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.91 ethambutol Not assoc w R
embC 4241845 c.1983T>C synonymous_variant 0.94 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245507 p.Gly759Arg missense_variant 0.12 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.93 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.94 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.87 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.89 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.89 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.9 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.92 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 0.9 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.91 streptomycin Not assoc w R