TB-Profiler result

Run: ERR9786244
Summary

Run ID: ERR9786244

Sample name:

Date: 2024-04-16T07:44:18.118545

Number of reads: 2763357

Percentage reads mapped: 99.64

Median coverage: 117.0

Strain: lineage4.1.2.1;lineage4.6.2.2;lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.41
lineage4.6.2 Euro-American RD726 0.37
lineage4.1 Euro-American None 0.44
lineage6.3 West-Africa 2 RD702 0.14
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.41
lineage4.1.2 Euro-American None 0.41
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.45
lineage4 Euro-American None 0.84
lineage6.3.1 West-Africa 2 RD702 0.16
lineage6 West-Africa 2 RD702 0.14
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 6446 p.Ala403Ser missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 0.16 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 13460 c.99T>C synonymous_variant 0.17 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.15 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.38 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491668 p.Lys296Glu missense_variant 0.22 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.15 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.38 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619628 c.-263G>A upstream_gene_variant 0.11 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.17 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.41 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.17 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoB 759765 c.-42A>G upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.42 rifampicin Not assoc w R
rpoB 760969 p.Ser388Leu missense_variant 0.13 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.21 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.44 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 0.19 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 0.33 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800544 c.-265G>A upstream_gene_variant 0.19 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.18 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.17 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475991 n.2334T>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
inhA 1674434 p.Val78Ala missense_variant 0.19 ethionamide Uncertain significance
isoniazid 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 2063187 c.1542C>T synonymous_variant 0.47 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.15 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.22 isoniazid Not assoc w R
katG 2155389 c.723C>G synonymous_variant 0.47 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.41 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222852 p.Ala105Thr missense_variant 0.14 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290090 c.-849C>T upstream_gene_variant 0.42 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.44 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.16 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.11 capreomycin
Rv2680 2996208 p.Ala35Asp missense_variant 0.4 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.37 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.19 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.68 cycloserine
ald 3087084 c.266delA frameshift_variant 0.16 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.38 ethionamide Uncertain significance
Rv3083 3449781 c.1278G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv3236c 3612571 c.546C>T synonymous_variant 0.38 pyrazinamide Not assoc w R
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.13 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.14 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 0.52 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.47 bedaquiline
rifampicin
glpK 4138377 p.Val460Ala missense_variant 0.12 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 4239298 c.-565C>T upstream_gene_variant 0.47 ethambutol Not assoc w R
embC 4239419 c.-444G>A upstream_gene_variant 0.49 ethambutol Uncertain significance
embC 4239923 p.Asp21Asn missense_variant 0.17 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.16 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.13 ethambutol Not assoc w R
embC 4242550 c.2688C>G synonymous_variant 0.31 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 0.39 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.15 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.15 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.15 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.14 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.11 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.17 ethionamide Uncertain significance
ethA 4326739 c.735C>G synonymous_variant 0.25 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.31 ethionamide Not assoc w R - Interim
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
whiB6 4338803 c.-282G>C upstream_gene_variant 0.12 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.14 streptomycin Not assoc w R