TB-Profiler result

Run: ERR386958
Summary

Run ID: ERR386958

Sample name:

Date: 2024-04-16T07:12:13.119728

Number of reads: 7124140

Percentage reads mapped: 99.43

Median coverage: 160.0

Strain: lineage1.2.1.1;lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.1 Indo-Oceanic RD239 0.47
lineage4.1 Euro-American None 0.48
lineage4.1.1.1 Euro-American (X-type) RD183 0.47
lineage4 Euro-American None 0.48
lineage4.1.1 Euro-American (X-type) None 0.48
lineage1 Indo-Oceanic RD239 0.48
lineage1.2.1 Indo-Oceanic RD239 0.54
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 fbiC p.Gly310* Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303858 p.Gly310* stop_gained 0.49 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 0.5 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 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.47 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 13189 p.Val124Met missense_variant 0.46 isoniazid Uncertain significance
Rv0010c 13298 p.Ile87Met missense_variant 0.53 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.38 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.5 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.46 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.49 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.53 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.55 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.47 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.57 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 775746 p.Met912Thr missense_variant 0.51 clofazimine
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.51 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 0.52 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.49 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.51 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254576 c.-42C>T upstream_gene_variant 0.53 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.44 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.48 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.49 ethambutol
atpE 1460853 c.-192T>G upstream_gene_variant 0.57 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.45 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 0.45 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063487 c.1242G>A synonymous_variant 0.5 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 0.46 isoniazid Not assoc w R
katG 2155144 p.Asn323Ser missense_variant 0.36 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.61 pyrazinamide Not assoc w R
PPE35 2168533 p.Val694Leu missense_variant 0.46 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.5 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
pncA 2290129 c.-888C>A upstream_gene_variant 0.51 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.46 isoniazid
kasA 2519035 c.921C>T synonymous_variant 0.48 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.54 isoniazid
thyA 3073863 c.609T>C synonymous_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.53 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.44 ethionamide Uncertain significance
Rv3083 3448835 p.Ser111Ile missense_variant 0.51 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.56 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640557 c.15T>C synonymous_variant 0.58 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiA 3641412 c.870G>A synonymous_variant 0.52 clofazimine Not assoc w R - Interim
pretomanid
delamanid
fbiA 3641447 p.Thr302Met missense_variant 0.48 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.61 rifampicin Not assoc w R
rpoA 3878601 c.-95delG upstream_gene_variant 0.2 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.44 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 0.49 ethambutol Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.53 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.42 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 0.61 ethambutol Not assoc w R
embA 4244420 c.1188G>C synonymous_variant 0.5 ethambutol Not assoc w R
embA 4244610 p.Ala460Thr missense_variant 0.46 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.55 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.45 ethambutol Not assoc w R
embB 4248515 p.Val668Ile missense_variant 0.52 ethambutol Not assoc w R - Interim
embB 4249352 c.2839C>A synonymous_variant 0.51 ethambutol Not assoc w R - Interim
embB 4249408 c.2895G>A synonymous_variant 0.49 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.53 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.55 ethambutol Not assoc w R
ethA 4327360 c.114G>C synonymous_variant 0.49 ethionamide Not assoc w R - Interim
whiB6 4338361 p.Arg54Gln missense_variant 0.56 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 0.55 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 0.55 streptomycin Not assoc w R
gid 4407781 p.Ala141Glu missense_variant 0.49 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.49 streptomycin Not assoc w R
gid 4407995 p.Ser70Arg missense_variant 0.54 streptomycin Uncertain significance