TB-Profiler result

Run: b416ea88-9ce8-4c7f-a8ea-8b7ca4f7b25a
Summary

Run ID: b416ea88-9ce8-4c7f-a8ea-8b7ca4f7b25a

Sample name:

Date: 22-02-2024 23:28:37

Number of reads: 178168

Percentage reads mapped: 70.85

Median coverage: 5

Strain: lineage4;La1.8.1

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
La1 M.bovis None 0.96
La1.8.1 M.bovis None 0.94
lineage4 Euro-American None 0.09
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 5089 c.-151A>T upstream_gene_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 5416 c.177C>T synonymous_variant 0.17 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8285 c.984C>T synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8354 c.1053G>C synonymous_variant 0.1 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8390 c.1089C>G synonymous_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8391 p.Tyr364Leu missense_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8399 c.1098T>G synonymous_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8408 c.1107A>G synonymous_variant 0.17 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8414 c.1113C>T synonymous_variant 0.15 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8420 c.1119T>C synonymous_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8504 c.1203G>C synonymous_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8510 c.1209G>A synonymous_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8513 c.1212C>G synonymous_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8516 c.1215T>C synonymous_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8519 c.1218A>G synonymous_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8520 c.1219C>T synonymous_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9217 p.Asp639Ala missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491160 c.378G>A synonymous_variant 0.12 delamanid
rpoB 760283 c.477G>C synonymous_variant 0.3 rifampicin
rpoB 760316 c.510C>G synonymous_variant 0.3 rifampicin
rpoB 760415 c.609C>T synonymous_variant 0.36 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.31 rifampicin
rpoB 760430 c.624T>C synonymous_variant 0.25 rifampicin
rpoB 760433 c.627C>T synonymous_variant 0.25 rifampicin
rpoB 761147 c.1341C>T synonymous_variant 0.17 rifampicin
rpoB 761150 c.1344A>T synonymous_variant 0.17 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.18 rifampicin
rpoB 761180 c.1374A>C synonymous_variant 0.15 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.15 rifampicin
rpoB 761195 c.1389G>C synonymous_variant 0.17 rifampicin
rpoB 761198 c.1392G>T synonymous_variant 0.17 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.2 rifampicin
rpoB 761217 p.Pro471Ser missense_variant 0.2 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.17 rifampicin
rpoB 761240 c.1434C>T synonymous_variant 0.17 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.17 rifampicin
rpoC 762833 c.-537C>T upstream_gene_variant 0.2 rifampicin
rpoC 762839 c.-531G>A upstream_gene_variant 0.2 rifampicin
rpoC 762857 c.-513C>G upstream_gene_variant 0.2 rifampicin
rpoC 762863 c.-507T>C upstream_gene_variant 0.18 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.17 rifampicin
rpoC 762917 c.-453C>G upstream_gene_variant 0.12 rifampicin
rpoC 762920 c.-450C>T upstream_gene_variant 0.12 rifampicin
rpoC 762929 c.-441G>C upstream_gene_variant 0.17 rifampicin
rpoC 763103 c.-267G>C upstream_gene_variant 0.17 rifampicin
rpoC 763115 c.-255T>C upstream_gene_variant 0.14 rifampicin
rpoC 763127 c.-243G>C upstream_gene_variant 0.13 rifampicin
rpoC 763130 c.-240G>A upstream_gene_variant 0.13 rifampicin
rpoC 763133 c.-237G>C upstream_gene_variant 0.13 rifampicin
rpoC 763136 c.-234C>T upstream_gene_variant 0.13 rifampicin
rpoC 763142 c.-228C>G upstream_gene_variant 0.13 rifampicin
rpoC 763160 c.-210G>T upstream_gene_variant 0.15 rifampicin
rpoC 763166 c.-204A>G upstream_gene_variant 0.18 rifampicin
rpoC 763486 c.117T>C synonymous_variant 0.2 rifampicin
mmpL5 775924 c.2557C>T synonymous_variant 0.17 clofazimine
bedaquiline
rpsL 781728 c.169T>C synonymous_variant 0.2 streptomycin
rpsL 781732 c.174_177delGAGT frameshift_variant 0.2 streptomycin
rpsL 781739 c.180_181insCGGC frameshift_variant 0.2 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.2 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.2 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.2 streptomycin
rpsL 781772 c.213C>T synonymous_variant 0.36 streptomycin
fbiC 1303382 p.Pro151Leu missense_variant 0.11 delamanid
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.2 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.2 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.22 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.22 linezolid
kanamycin Uncertain significance
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11 linezolid
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
aminoglycosides
streptomycin
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.3 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.4 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.4 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.4 linezolid
kanamycin
capreomycin
amikacin Uncertain significance
aminoglycosides
streptomycin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5 linezolid
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
aminoglycosides
streptomycin
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.4 linezolid
inhA 1674024 c.-178T>C upstream_gene_variant 0.2 ethionamide
isoniazid
fabG1 1674037 p.Gln200Ala missense_variant 0.2 ethionamide
isoniazid
fabG1 1674049 p.Gln204Asp missense_variant 0.2 ethionamide
isoniazid
inhA 1674054 c.-148T>C upstream_gene_variant 0.2 ethionamide
isoniazid
rpsA 1833949 c.408T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.2 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.23 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.23 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.23 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.25 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.25 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.2 pyrazinamide
rpsA 1834150 c.609G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834153 c.612T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834154 p.Asn205Gln missense_variant 0.23 pyrazinamide
rpsA 1834157 c.616T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834162 c.621A>G synonymous_variant 0.25 pyrazinamide
rpsA 1834165 c.624A>G synonymous_variant 0.25 pyrazinamide
rpsA 1834169 p.Thr210Ala missense_variant 0.25 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.21 pyrazinamide
rpsA 1834189 c.648G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834213 c.672G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834246 c.705G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834252 c.711C>G synonymous_variant 0.32 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.37 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.35 pyrazinamide
rpsA 1834279 c.738C>T synonymous_variant 0.29 pyrazinamide
rpsA 1834297 c.756C>T synonymous_variant 0.4 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.4 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.27 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.27 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.2 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834619 c.1078T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.2 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.2 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.2 pyrazinamide
kasA 2517941 c.-174C>G upstream_gene_variant 0.18 isoniazid
kasA 2517959 c.-156C>T upstream_gene_variant 0.2 isoniazid
kasA 2517962 c.-153C>G upstream_gene_variant 0.18 isoniazid
fprA 3474427 p.Val141Ile missense_variant 0.8 capreomycin Uncertain significance
amikacin Uncertain significance
fbiB 3641803 c.271delC frameshift_variant 0.18 delamanid
rpoA 3877704 c.804G>T synonymous_variant 0.18 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.18 rifampicin
rpoA 3877926 c.582G>C synonymous_variant 0.17 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.2 rifampicin
rpoA 3877971 p.Asp179Glu missense_variant 0.18 rifampicin
clpC1 4038647 c.2058T>G synonymous_variant 0.5 pyrazinamide
clpC1 4038679 p.Pro676Ala missense_variant 0.5 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.5 pyrazinamide
clpC1 4038695 c.2010C>G synonymous_variant 0.5 pyrazinamide
clpC1 4039541 c.1164C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039544 c.1161C>T synonymous_variant 0.2 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.18 pyrazinamide
clpC1 4040342 c.363C>A synonymous_variant 0.25 pyrazinamide
clpC1 4040348 c.357G>C synonymous_variant 0.27 pyrazinamide
clpC1 4040354 c.351A>G synonymous_variant 0.25 pyrazinamide
clpC1 4040357 c.348T>C synonymous_variant 0.25 pyrazinamide
clpC1 4040363 c.342A>T synonymous_variant 0.25 pyrazinamide
clpC1 4040366 c.339C>T synonymous_variant 0.25 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.23 pyrazinamide
clpC1 4040372 c.333C>T synonymous_variant 0.25 pyrazinamide
clpC1 4040375 c.330G>C synonymous_variant 0.31 pyrazinamide
clpC1 4040380 c.325T>C synonymous_variant 0.29 pyrazinamide
clpC1 4040387 c.318A>G synonymous_variant 0.27 pyrazinamide
clpC1 4040393 c.312G>C synonymous_variant 0.36 pyrazinamide
clpC1 4040411 c.294T>C synonymous_variant 0.29 pyrazinamide
clpC1 4040423 c.282A>G synonymous_variant 0.25 pyrazinamide
clpC1 4040431 c.274T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040433 c.271_272delAGinsTC synonymous_variant 0.18 pyrazinamide
clpC1 4040441 c.264C>G synonymous_variant 0.18 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.2 pyrazinamide
clpC1 4040459 c.246C>G synonymous_variant 0.2 pyrazinamide
clpC1 4040462 c.243C>G synonymous_variant 0.2 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040468 c.237G>C synonymous_variant 0.18 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040477 c.228G>T synonymous_variant 0.18 pyrazinamide
clpC1 4040480 c.225T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040486 c.219G>A synonymous_variant 0.17 pyrazinamide
clpC1 4040495 c.210C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040522 c.183T>C synonymous_variant 0.17 pyrazinamide
aftB 4269351 c.-515C>T upstream_gene_variant 1.0 capreomycin
amikacin
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269602 p.Val78Ile missense_variant 1.0 ethambutol Uncertain significance