TB-Profiler result

Run: ERR2432997
Summary

Run ID: ERR2432997

Sample name:

Date: 2024-03-27T00:37:58.940014

Number of reads: 700233

Percentage reads mapped: 76.66

Median coverage: 30.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
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 rrs n.514A>C Assoc w R
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.83 streptomycin 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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761105 c.1299C>T synonymous_variant 0.88 rifampicin Not assoc w R - Interim
rpoC 762947 c.-423C>G upstream_gene_variant 0.24 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.24 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763052 c.-318G>C upstream_gene_variant 0.18 rifampicin
rpoB 763053 c.3247_3249delTTGinsCC frameshift_variant&missense_variant 0.18 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763072 c.3268_3270delACC conservative_inframe_deletion 0.16 rifampicin
rpoB 763078 c.3272_3273insGCC disruptive_inframe_insertion 0.17 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.2 rifampicin Uncertain significance
rpoC 764716 c.1347G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764722 c.1353G>C synonymous_variant 0.16 rifampicin
rpoC 764746 c.1377G>C synonymous_variant 0.17 rifampicin
rpoC 764749 c.1380G>C synonymous_variant 0.17 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.17 rifampicin
rpoC 764785 c.1416C>G synonymous_variant 0.18 rifampicin
rpoC 764797 c.1428G>C synonymous_variant 0.17 rifampicin
rpoC 764804 p.Gln479Ala missense_variant 0.14 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.14 rifampicin
rpoC 764813 p.Gln482Val missense_variant 0.13 rifampicin
rpoC 764824 c.1455T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.15 rifampicin
rpoC 764843 p.Ala492Thr missense_variant 0.16 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
Rv1258c 1406302 c.1039C>A synonymous_variant 1.0 streptomycin
isoniazid Not assoc w R - Interim
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGCCAG non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.29 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2715535 c.-985_-204del upstream_gene_variant 1.0 amikacin
kanamycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
whiB7 3569111 c.-432T>C upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
clpC1 4039691 c.1014G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039711 p.Ile332Val missense_variant 0.12 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.2 pyrazinamide
clpC1 4039820 c.885T>G synonymous_variant 0.21 pyrazinamide
clpC1 4039829 c.874_876delTTGinsCC frameshift_variant&missense_variant 0.22 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.22 pyrazinamide
clpC1 4039838 c.865_867delCTGinsAC frameshift_variant&missense_variant 0.23 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039871 c.834C>G synonymous_variant 0.23 pyrazinamide
clpC1 4039875 p.Asn277Arg missense_variant 0.24 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.3 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039925 c.780C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039945 p.Ser254Ala missense_variant 0.24 pyrazinamide
clpC1 4039946 c.759A>C synonymous_variant 0.24 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039955 c.750G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039979 c.726C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039988 c.717C>G synonymous_variant 0.28 pyrazinamide
clpC1 4039994 p.Glu237Asp missense_variant 0.28 pyrazinamide
clpC1 4040001 p.His235Arg missense_variant 0.24 pyrazinamide
clpC1 4040010 p.Ala232Asp missense_variant 0.28 pyrazinamide Uncertain significance
clpC1 4040018 c.687G>C synonymous_variant 0.25 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.27 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.21 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol 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