TB-Profiler result

Run: ERR4815515
Summary

Run ID: ERR4815515

Sample name:

Date: 2024-03-26T16:05:29.241597

Number of reads: 2002534

Percentage reads mapped: 84.18

Median coverage: 45.0

Strain: lineage1.1.2;lineage4.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.65
lineage1.1.2 Indo-Oceanic RD239 0.2
lineage4.1 Euro-American None 0.72
lineage1.1 Indo-Oceanic RD239 0.21
lineage4 Euro-American None 0.71
lineage1 Indo-Oceanic RD239 0.23
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 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.22 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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8435 c.1134C>G synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.22 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575376 p.Ser10Leu missense_variant 0.26 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.69 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.19 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.2 rifampicin Not assoc w R
nusG 734475 c.222T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
nusG 734532 c.279A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.13 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760406 c.600G>C synonymous_variant 0.16 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.15 rifampicin
rpoB 761354 c.1548C>T synonymous_variant 0.15 rifampicin
rpoB 762014 c.2208C>T synonymous_variant 0.13 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764815 c.1446A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.74 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.28 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 0.21 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
rpsL 781421 c.-139C>A upstream_gene_variant 0.79 streptomycin Uncertain significance
rplC 800357 c.-452C>A upstream_gene_variant 0.17 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304610 c.1680C>T synonymous_variant 0.72 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304916 c.1986T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1304928 c.1998T>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304937 c.2007G>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1304958 c.2028T>G synonymous_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1304983 c.2053C>T synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304994 c.2064A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
embR 1417019 p.Cys110Tyr missense_variant 0.21 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.17 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833661 c.120A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.15 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.44 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.3 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.95 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 0.24 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 0.23 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.23 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.2 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 0.2 isoniazid
Rv2477c 2783665 c.378A>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.34 capreomycin Not assoc w R
Rv2752c 3066376 c.-185C>T upstream_gene_variant 0.21 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624660 p.Ala84Gly missense_variant 0.67 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039694 c.1011G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.24 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 4241042 p.Asn394Asp missense_variant 0.26 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 0.64 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.29 ethambutol Not assoc w R
embA 4245182 c.1950T>C synonymous_variant 0.14 ethambutol
embA 4245189 c.1957C>T synonymous_variant 0.15 ethambutol
embA 4245198 p.Leu656Ile missense_variant 0.14 ethambutol
embB 4247356 c.843C>T synonymous_variant 0.26 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.18 ethambutol Not assoc w R
aftB 4268683 p.Gly52Ser missense_variant 0.62 ethambutol Uncertain significance
ubiA 4269606 c.228T>C synonymous_variant 0.16 ethambutol Not assoc w R
whiB6 4338441 p.Tyr27* stop_gained 0.3 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338449 p.Ala25Pro missense_variant 0.32 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 0.19 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
gid 4407873 c.330G>T synonymous_variant 0.18 streptomycin Not assoc w R