TB-Profiler result

Run: ERR7451300
Summary

Run ID: ERR7451300

Sample name:

Date: 2024-04-14T12:28:27.574729

Number of reads: 343730

Percentage reads mapped: 96.99

Median coverage: 10.0

Strain: M.canetti

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
M.canetti M.canetti None 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
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 5452 c.213G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6454 c.1215C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6721 c.1482C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 7835 c.534A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7937 c.636A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8039 c.738T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8054 c.753T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8198 c.897T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8219 c.918T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8399 c.1098T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8756 c.1455A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8966 c.1665C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9817 c.2517_*53delANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 490666 c.-117G>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 490687 c.-96T>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491181 c.399T>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491191 p.Gly137Arg missense_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491196 c.414A>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491212 p.Ser144Arg missense_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575665 c.318G>C synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
hadA 731852 c.-78A>G upstream_gene_variant 1.0 isoniazid
hadA 732379 c.450A>G synonymous_variant 1.0 isoniazid Not assoc w R - Interim
rpoB 759741 c.-66C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 764152 c.783C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 779283 c.-803G>A upstream_gene_variant 1.0 clofazimine
bedaquiline
mmpL5 779295 c.-815A>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781456 c.-104A>G upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800111 c.-698C>T upstream_gene_variant 1.0 linezolid
rplC 800155 c.-654_-653insG upstream_gene_variant 1.0 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 1.0 linezolid
rplC 801267 c.459A>G synonymous_variant 1.0 linezolid Not assoc w R - Interim
Rv1129c 1254602 c.-68C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1303695 c.765T>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304598 c.1668C>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1364547 c.135G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1258c 1406466 p.Ser292Leu missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1406492 c.849C>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
embR 1417454 c.-107C>A upstream_gene_variant 1.0 ethambutol
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1418025 c.-678G>A upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471850 n.5_6delGTinsTGG non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474438 n.781A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
fabG1 1673257 c.-183C>G upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1834169 p.Thr210Ala missense_variant 1.0 pyrazinamide Uncertain significance
tlyA 1917606 c.-334G>C upstream_gene_variant 1.0 capreomycin
bacA 2064378 c.351C>T synonymous_variant 1.0 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 2156055 c.57C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2156658 c.-547A>G upstream_gene_variant 1.0 isoniazid
PPE35 2169686 c.927T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2169717 p.Asn299Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170232 c.381T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2170394 c.219G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2170485 p.Val43Ala missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170694 c.-82T>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170720 c.-108A>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170847 c.-235T>C upstream_gene_variant 1.0 pyrazinamide
PPE35 2170860 c.-248A>C upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223318 c.-154A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289104 c.138A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
pncA 2289700 c.-459T>C upstream_gene_variant 1.0 pyrazinamide
pncA 2289827 c.-586A>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2783425 c.618C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ribD 2986929 p.Leu31Phe missense_variant 1.0 para-aminosalicylic_acid
Rv2680 2996440 c.336G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2752c 3064578 c.1614C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3066687 c.-496G>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3074238 c.234C>T synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3074247 c.225C>T synonymous_variant 1.0 para-aminosalicylic_acid
ald 3087122 c.303T>C synonymous_variant 1.0 cycloserine
ald 3087140 c.321G>A synonymous_variant 1.0 cycloserine
fbiD 3339402 c.285C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448349 c.-155C>T upstream_gene_variant 1.0 ethionamide
Rv3083 3448453 c.-51G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448474 c.-30G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448481 c.-23G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448484 c.-20T>C upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448487 c.-17T>G upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448495 c.-9G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3448545 c.42A>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3448588 p.Asp29Asn missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3448606 c.103C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3448611 c.108A>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB7 3568687 c.-8A>T upstream_gene_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612709 c.408G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrA 3627190 c.160T>C synonymous_variant 1.0 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627802 c.-453T>C upstream_gene_variant 1.0 bedaquiline
rifampicin
mtrA 3627831 c.-482T>C upstream_gene_variant 1.0 bedaquiline
rifampicin
mtrA 3627839 c.-490T>C upstream_gene_variant 1.0 bedaquiline
rifampicin
fbiB 3642254 c.720G>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3642467 c.933T>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3642852 p.Pro440Ser missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiB 3642874 p.Leu447Arg missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
alr 3840527 c.894A>C synonymous_variant 1.0 cycloserine
alr 3840620 c.801T>C synonymous_variant 1.0 cycloserine
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
alr 3840796 p.Asp209Asn missense_variant 1.0 cycloserine
alr 3840994 p.His143Asp missense_variant 1.0 cycloserine
alr 3841172 c.249A>C synonymous_variant 1.0 cycloserine
alr 3841419 p.Val1Ala missense_variant 1.0 cycloserine
rpoA 3877527 c.981C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877740 c.768G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877886 c.622C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877887 c.621G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878848 c.-341C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3879193 c.-686G>A upstream_gene_variant 1.0 rifampicin
ddn 3986910 c.67C>A synonymous_variant 1.0 delamanid
pretomanid
ddn 3987050 c.207C>T synonymous_variant 1.0 delamanid
pretomanid
clpC1 4038443 c.2262G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038746 c.1959C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038779 c.1926C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038848 c.1857C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038860 c.1845G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039046 c.1659C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039058 c.1647C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039094 c.1611C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039100 c.1605C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039336 c.1369C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039352 c.1353C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039448 c.1257A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039454 c.1251A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039502 c.1203C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040045 c.660C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040048 c.657C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040063 c.642G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040090 c.615T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040093 c.612C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040267 c.438A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040273 c.432T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040276 c.429C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040279 c.426C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040450 c.255A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040471 c.234T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040480 c.225T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040534 c.171A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040551 c.154T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040573 c.132T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040657 c.48T>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
panD 4043932 p.Met117Thr missense_variant 1.0 pyrazinamide Uncertain significance
panD 4044243 c.39C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 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
glpK 4139183 c.572dupG frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139813 c.-58T>G upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239764 c.-99G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embA 4244154 p.Thr308Pro missense_variant 1.0 ethambutol Uncertain significance
embA 4245023 c.1791A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247590 c.1077A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248195 p.Lys561Met missense_variant 1.0 ethambutol Uncertain significance
embB 4248206 p.Ser565Gly missense_variant 1.0 ethambutol Uncertain significance
embB 4248439 c.1926C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248664 c.2151G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248721 c.2208C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248744 p.Val744Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4248853 c.2340G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4268331 p.Gln169Pro missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ethA 4326463 c.1011C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4326740 p.Arg245His missense_variant 1.0 ethionamide Uncertain significance
ethR 4327547 c.-2_-1insA upstream_gene_variant 1.0 ethionamide Uncertain significance
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 4338741 c.-220A>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338785 c.-266_-264delGGCinsAG upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408185 c.18C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim