TB-Profiler result

Run: ERR161077
Summary

Run ID: ERR161077

Sample name:

Date: 2024-04-16T09:20:18.571535

Number of reads: 3431983

Percentage reads mapped: 99.3

Median coverage: 73.0

Strain: lineage1.1.3.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.8
lineage1.1.3.2 Indo-Oceanic RD239 0.8
lineage4.1 Euro-American None 0.17
lineage1.1 Indo-Oceanic RD239 0.79
lineage4.1.1.3 Euro-American (X-type) RD193 0.23
lineage4 Euro-American None 0.2
lineage4.1.1 Euro-American (X-type) None 0.18
lineage1 Indo-Oceanic RD239 0.76
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
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
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 0.79 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 8188 p.Leu296Pro missense_variant 0.78 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.79 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 0.83 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.76 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.79 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619695 c.-196G>A upstream_gene_variant 0.75 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 0.18 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.69 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.84 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.23 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.76 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.8 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 0.88 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 800219 c.-590T>C upstream_gene_variant 0.26 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.73 linezolid Not assoc w R
rplC 801166 p.Gly120Ser missense_variant 0.83 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.82 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407055 c.285delG frameshift_variant 0.76 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.82 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.83 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.73 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674883 p.Ile228Val missense_variant 0.8 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.77 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.81 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 0.68 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064420 c.309C>T synonymous_variant 0.79 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 0.84 isoniazid Not assoc w R
katG 2156096 p.Pro6Ser missense_variant 0.31 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.76 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.84 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 0.7 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89 isoniazid
ribD 2987589 c.751C>T synonymous_variant 0.21 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.81 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
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.79 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.72 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625783 c.-873C>T upstream_gene_variant 0.73 bedaquiline
rifampicin
fbiB 3642173 c.639G>A synonymous_variant 0.86 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rpoA 3878687 c.-180A>C upstream_gene_variant 0.77 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.68 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 4238874 c.-989A>C upstream_gene_variant 0.76 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.9 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.75 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 0.21 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.78 ethambutol Not assoc w R
embA 4244255 c.1023T>G synonymous_variant 0.77 ethambutol
embA 4245025 p.His598Arg missense_variant 0.73 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.77 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.75 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.22 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.77 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.77 ethambutol 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 0.76 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 0.75 streptomycin Not assoc w R
gid 4407661 p.Ser181Leu missense_variant 0.79 streptomycin Uncertain significance
gid 4407780 c.423G>A synonymous_variant 0.79 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.8 streptomycin Not assoc w R