TB-Profiler result

Run: 2b97a155-0177-4245-aff6-cd62af834a0c
Summary

Run ID: 2b97a155-0177-4245-aff6-cd62af834a0c

Sample name:

Date: 08-05-2024 18:45:19

Number of reads: 6929253

Percentage reads mapped: 97.66

Median coverage: 175

Strain: lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6 West-Africa 2 RD702 0.99
lineage6.3 West-Africa 2 RD702 1.0
lineage6.3.1 West-Africa 2 RD702 0.99
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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 0.98 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.99 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 490751 c.-32T>G upstream_gene_variant 0.12 delamanid
fgd1 491668 p.Lys296Glu missense_variant 0.99 delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
ccsA 620748 c.858T>G synonymous_variant 0.12 capreomycin
amikacin
rpoB 760969 p.Ser388Leu missense_variant 1.0 rifampicin Uncertain significance
rpoB 761723 p.Glu639Asp missense_variant 1.0 rifampicin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 765273 p.Val635Gly missense_variant 0.12 rifampicin
rpoC 766632 p.Val1088Gly missense_variant 0.21 rifampicin
rpoC 767314 p.Tyr1315* stop_gained 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Uncertain significance
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 delamanid Uncertain significance
fbiC 1304159 p.Val410Gly missense_variant 0.14 delamanid
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.12 streptomycin
pyrazinamide
isoniazid
atpE 1461083 c.39T>G synonymous_variant 0.12 bedaquiline
atpE 1461251 c.207G>T synonymous_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473945 n.288T>G non_coding_transcript_exon_variant 0.11 linezolid
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.12 linezolid
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.14 linezolid
inhA 1674434 p.Val78Ala missense_variant 0.99 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674952 p.Pro251Ala missense_variant 0.12 ethionamide
isoniazid
inhA 1674958 p.Thr253Ala missense_variant 0.12 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102694 p.Val117Ile missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Uncertain significance
katG 2155503 c.609C>T synonymous_variant 0.98 isoniazid
katG 2155778 p.Thr112Pro missense_variant 0.13 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168731 p.Pro628Thr missense_variant 1.0 pyrazinamide
PPE35 2169862 p.Asn251His missense_variant 0.12 pyrazinamide
PPE35 2170118 c.495A>C synonymous_variant 0.11 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2288879 c.363G>A synonymous_variant 0.99 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.99 isoniazid
ahpC 2726338 p.Val49Gly missense_variant 0.2 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.15 isoniazid
pepQ 2859904 p.Val172Gly missense_variant 0.14 clofazimine
bedaquiline
ribD 2987323 p.Val162Gly missense_variant 0.14 para-aminosalicylic_acid
Rv2752c 3064562 p.Thr544Pro missense_variant 0.16 rifampicin
isoniazid
Rv2752c 3064745 p.Thr483Pro missense_variant 0.12 rifampicin
isoniazid
thyX 3067995 c.-50A>C upstream_gene_variant 0.14 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
fbiD 3339304 p.Thr63Pro missense_variant 0.18 delamanid
Rv3083 3449072 p.Val190Gly missense_variant 0.13 ethionamide
Rv3083 3449781 c.1278G>A synonymous_variant 1.0 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3475081 p.Trp359Gly missense_variant 0.14 capreomycin
amikacin
fprA 3475106 p.Val367Gly missense_variant 0.15 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 0.99 capreomycin Uncertain significance
amikacin Uncertain significance
rpoA 3877696 p.Thr271Ile missense_variant 1.0 rifampicin Uncertain significance
rpoA 3878580 c.-73A>C upstream_gene_variant 0.11 rifampicin
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Uncertain significance
embC 4241843 p.Leu661Ile missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 0.99 ethambutol
embC 4242822 p.Val987Gly missense_variant 0.12 ethambutol
embA 4244220 c.988C>T synonymous_variant 0.98 ethambutol
embA 4244379 p.Pro383Ser missense_variant 0.98 ethambutol Uncertain significance
embB 4246864 c.351C>T synonymous_variant 0.99 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.99 ethambutol Uncertain significance
aftB 4268477 c.360C>T synonymous_variant 0.99 capreomycin
amikacin
aftB 4269351 c.-515C>T upstream_gene_variant 1.0 capreomycin
amikacin
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
aftB 4269522 c.-686C>T upstream_gene_variant 0.99 capreomycin
amikacin
aftB 4269606 c.-770T>C upstream_gene_variant 1.0 capreomycin
amikacin
ethA 4326465 p.Ile337Val missense_variant 1.0 ethionamide Uncertain significance
ethR 4327642 p.Thr32Pro missense_variant 0.12 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin