TB-Profiler result

Run: ERR552306
Summary

Run ID: ERR552306

Sample name:

Date: 2024-04-14T14:34:49.397367

Number of reads: 304980

Percentage reads mapped: 97.22

Median coverage: 10.0

Strain: M.canetti;lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.9 Euro-American (H37Rv-like) None 0.52
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 mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
mmpR5 779431 c.442_444delAACinsCA frameshift_variant&missense_variant 1.0 clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 6721 c.1482C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 7093 c.1854T>C 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 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 8810 c.1509A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 8813 p.Asp504Glu missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8966 c.1665C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575216 c.-132C>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575665 c.318G>C synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
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 763660 c.291T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764152 c.783C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 1.0 rifampicin 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
mmpL5 779472 c.-992G>A upstream_gene_variant 1.0 clofazimine
bedaquiline
mmpS5 779523 c.-618T>A upstream_gene_variant 1.0 clofazimine
bedaquiline
mmpS5 779538 c.-633A>C upstream_gene_variant 1.0 clofazimine
bedaquiline
mmpS5 779539 c.-634C>A upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 800618 c.-191T>C upstream_gene_variant 1.0 linezolid
rplC 800970 c.162T>C synonymous_variant 1.0 linezolid Not assoc w R - Interim
Rv1129c 1254602 c.-68C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254654 c.-120A>G upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254678 c.-144A>G upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1302694 c.-237C>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1302810 c.-121C>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1302860 c.-71G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
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
embR 1417294 c.54A>G synonymous_variant 1.0 ethambutol 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 1417748 c.-401T>C 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
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917812 c.-128G>A upstream_gene_variant 1.0 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
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 2170232 c.381T>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
kasA 2519287 c.1173T>C synonymous_variant 1.0 isoniazid
eis 2714714 p.Ala207Thr missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
folC 2747572 c.27T>C synonymous_variant 1.0 para-aminosalicylic_acid
folC 2747575 c.24G>C synonymous_variant 1.0 para-aminosalicylic_acid
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
Rv2477c 2784328 c.-286C>T upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
pepQ 2859490 p.Val310Ala missense_variant 1.0 clofazimine
bedaquiline
Rv2680 2996440 c.336G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2680 2996578 c.474C>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2681 2997122 c.384A>G synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2681 2997293 c.555G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
Rv2752c 3064971 c.1221C>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
Rv2752c 3066905 c.-714T>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067980 c.-35T>C upstream_gene_variant 1.0 para-aminosalicylic_acid
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 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087122 c.303T>C synonymous_variant 1.0 cycloserine
ald 3087140 c.321G>A synonymous_variant 1.0 cycloserine
fbiD 3339049 c.-69C>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
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 3449868 c.1365C>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3449877 c.1374T>C synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3449885 p.Arg461Lys missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3611968 c.1149T>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3612211 c.906A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3612250 c.867A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3612301 c.816G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3612541 c.576G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3612561 p.Thr186Ala missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3612709 c.408G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3613056 c.61C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3626461 c.153A>G synonymous_variant 1.0 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627190 c.160T>C synonymous_variant 1.0 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627715 c.-366G>A upstream_gene_variant 1.0 bedaquiline
rifampicin Uncertain significance
mtrA 3627734 c.-385A>G upstream_gene_variant 1.0 bedaquiline
rifampicin
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
alr 3840796 p.Asp209Asn missense_variant 1.0 cycloserine
alr 3840914 c.507G>C synonymous_variant 1.0 cycloserine
alr 3840994 p.His143Asp missense_variant 1.0 cycloserine
alr 3841365 c.55_56insA frameshift_variant 1.0 cycloserine
alr 3841419 p.Val1Ala missense_variant 1.0 cycloserine
alr 3841539 c.-119C>T upstream_gene_variant 1.0 cycloserine
alr 3841546 c.-126C>G upstream_gene_variant 1.0 cycloserine
alr 3841568 c.-148G>A upstream_gene_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 3878848 c.-341C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878878 c.-371T>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878914 c.-407T>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878947 c.-440G>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878961 c.-454C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878962 c.-455G>A upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878998 c.-491C>G upstream_gene_variant 1.0 rifampicin Uncertain significance
ddn 3986910 c.67C>A synonymous_variant 1.0 delamanid
pretomanid
ddn 3987287 c.444T>C synonymous_variant 1.0 delamanid
pretomanid
clpC1 4038443 c.2262G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038683 c.2022T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038974 c.1731T>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 4039274 c.1431G>C 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 4039502 c.1203C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039682 c.1023C>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039700 c.1005C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039718 c.987C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039817 c.888A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039820 c.885T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039823 c.882T>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 4040363 c.342A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040393 c.312G>C 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 4040657 c.48T>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040879 c.-177_-175delTGGinsCGGT upstream_gene_variant 1.0 pyrazinamide
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
panD 4044533 c.-252T>C upstream_gene_variant 1.0 pyrazinamide
glpK 4138883 c.873C>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
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139321 c.435T>A 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
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139420 c.336T>C 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
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4239032 c.-831T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4239110 c.-753C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
embA 4243919 c.687G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embA 4244312 c.1080T>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 4247815 c.1302C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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 4249069 c.2556A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ubiA 4269588 c.246G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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
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
whiB6 4338878 c.-357C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4408185 c.18C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim