TB-Profiler result

Run: SRR2100184
Summary

Run ID: SRR2100184

Sample name:

Date: 2024-04-15T15:04:45.281038

Number of reads: 4697401

Percentage reads mapped: 99.38

Median coverage: 109.0

Strain: lineage1.1.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.78
lineage4.1 Euro-American None 0.25
lineage1.1 Indo-Oceanic RD239 0.76
lineage4.1.1.3 Euro-American (X-type) RD193 0.19
lineage4.1.1 Euro-American (X-type) None 0.22
lineage1 Indo-Oceanic RD239 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
isoniazid
ethambutol
pyrazinamide panD p.Ile49Val Uncertain significance Mutation from literature
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
rpoB 761109 p.Asp435Tyr missense_variant 0.26 rifampicin Assoc w R
panD 4044137 p.Ile49Val missense_variant 0.84 pyrazinamide Uncertain significance Mutation from literature
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
dnaA 1519 p.Arg507Cys missense_variant 0.73 isoniazid Uncertain significance
gyrB 5770 c.531C>T synonymous_variant 0.8 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.77 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 0.74 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 0.78 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 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.26 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.81 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.69 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.75 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.74 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.22 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.77 rifampicin Not assoc w R
rpoC 765190 c.1821G>A synonymous_variant 0.76 rifampicin Not assoc w R - Interim
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 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779434 p.Val149Ile missense_variant 0.75 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.22 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.78 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.81 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406503 p.Val280Leu missense_variant 0.79 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.69 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.84 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.8 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.82 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.83 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 0.76 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 0.79 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.83 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223170 c.-6G>A upstream_gene_variant 0.23 clofazimine
bedaquiline
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 0.76 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74 isoniazid
ribD 2987151 p.His105Tyr missense_variant 0.75 para-aminosalicylic_acid
Rv2681 2996912 c.174C>T synonymous_variant 0.77 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.68 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
Rv2752c 3065598 c.594G>A synonymous_variant 0.66 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
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 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878569 c.-63_-62insG upstream_gene_variant 0.82 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.72 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.79 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 0.82 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.74 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 0.18 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.74 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.85 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.25 ethambutol Not assoc w R
aftB 4267867 p.Leu324Met missense_variant 0.77 ethambutol Uncertain significance
aftB 4268461 p.Ile126Val missense_variant 0.8 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.76 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.78 ethambutol Not assoc w R
ubiA 4269630 c.204G>A synonymous_variant 0.71 ethambutol Not assoc w R - Interim
whiB6 4338596 c.-76_-75delAGinsC upstream_gene_variant 0.73 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338596 c.-75delG upstream_gene_variant 0.27 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338596 c.-76_-75delAGinsC upstream_gene_variant 0.73 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338596 c.-75delG upstream_gene_variant 0.27 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.75 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 0.8 streptomycin Not assoc w R
gid 4407798 c.405G>T synonymous_variant 0.29 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.71 streptomycin Not assoc w R