TB-Profiler result

Run: ERR123948
Summary

Run ID: ERR123948

Sample name:

Date: 2024-04-16T06:48:43.995647

Number of reads: 4284737

Percentage reads mapped: 99.47

Median coverage: 98.0

Strain: lineage4.1.1.3;lineage5.1.2

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.83
lineage5.1.2 West-Africa 1 RD711 0.14
lineage4.1.1.3 Euro-American (X-type) RD193 0.85
lineage4 Euro-American None 0.84
lineage4.1.1 Euro-American (X-type) None 0.82
lineage5 West-Africa 1 RD711 0.16
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
streptomycin
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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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 0.15 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)
rpoB 761109 p.Asp435Tyr missense_variant 0.64 rifampicin 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
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 9143 c.1842T>C synonymous_variant 0.1 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
gyrA 9566 c.2265C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.2 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.27 isoniazid Uncertain significance
fgd1 491035 p.Val85Ile missense_variant 0.12 clofazimine
pretomanid
delamanid
fgd1 491216 p.Gly145Ala missense_variant 0.12 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.11 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.93 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.22 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.19 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.82 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 0.14 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 0.86 linezolid
fbiC 1302899 c.-32A>G upstream_gene_variant 0.17 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406382 p.Val320Ala missense_variant 0.15 streptomycin
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 0.16 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.13 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673338 c.-102G>A upstream_gene_variant 0.12 ethionamide
isoniazid
rpsA 1834957 c.1416C>T synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tsnR 1853565 c.-41G>A upstream_gene_variant 0.2 linezolid Uncertain significance
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 0.13 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
PPE35 2170265 c.347delG frameshift_variant 0.15 pyrazinamide Uncertain significance
Rv1979c 2223170 c.-6G>A upstream_gene_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
ald 3087084 c.266delA frameshift_variant 0.15 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 0.21 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.19 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840932 c.489C>T synonymous_variant 0.16 cycloserine
rpoA 3878493 c.15G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 0.25 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 0.15 delamanid Uncertain significance
pretomanid
glpK 4138377 p.Val460Ala missense_variant 0.11 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 4139131 p.Glu209Lys missense_variant 0.14 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 0.13 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.88 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 0.17 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 0.14 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.1 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.91 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.12 ethambutol Not assoc w R
ethA 4326928 c.546C>T synonymous_variant 0.14 ethionamide Not assoc w R - Interim
ethR 4326976 c.-573G>A upstream_gene_variant 0.18 ethionamide
ethA 4327103 p.Gly124Asp missense_variant 0.17 ethionamide 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407798 c.405G>T synonymous_variant 0.87 streptomycin Not assoc w R