TB-Profiler result

Run: 66210e2c-f545-4de3-94c5-d3b4040bc62e
Summary

Run ID: 66210e2c-f545-4de3-94c5-d3b4040bc62e

Sample name:

Date: 29-01-2024 00:20:28

Number of reads: 457362

Percentage reads mapped: 96.11

Median coverage: 12

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) RD105;RD207 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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rrs n.888G>A Uncertain significance
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
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 6542 p.Ile435Leu missense_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 8444 c.1143G>A synonymous_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8544 p.Asp415Asn missense_variant 0.11 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9265 p.Asp655Ala missense_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9357 p.Thr686Pro missense_variant 0.17 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9562 p.Met754Lys missense_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490624 c.-159T>G upstream_gene_variant 0.17 delamanid
fgd1 490751 c.-32T>G upstream_gene_variant 0.14 delamanid
fgd1 490865 p.Glu28Ala missense_variant 0.11 delamanid
fgd1 490981 p.Arg67Trp missense_variant 0.14 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.18 delamanid
fgd1 491623 p.Ala281Thr missense_variant 0.18 delamanid
mshA 575740 c.393G>A synonymous_variant 0.14 ethionamide
isoniazid
mshA 575752 c.405G>A synonymous_variant 0.13 ethionamide
isoniazid
ccsA 620159 p.Leu90Arg missense_variant 0.15 capreomycin
amikacin
ccsA 620651 p.Ala254Val missense_variant 0.15 capreomycin
amikacin
rpoB 760790 c.984C>A synonymous_variant 0.11 rifampicin
rpoB 762022 p.Asp739Val missense_variant 0.11 rifampicin
rpoB 762196 p.Val797Gly missense_variant 0.13 rifampicin
rpoC 762455 c.-915C>T upstream_gene_variant 0.15 rifampicin
rpoB 762540 p.Asn912Asp missense_variant 0.12 rifampicin
rpoB 762694 p.Asn963Thr missense_variant 0.11 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 763411 c.42T>A synonymous_variant 0.13 rifampicin
rpoC 763710 c.345delG frameshift_variant 0.1 rifampicin
rpoC 764468 p.Val367Phe missense_variant 0.17 rifampicin
rpoC 764574 p.Leu402Pro missense_variant 0.2 rifampicin
rpoC 764935 p.Ile522Met missense_variant 0.15 rifampicin
rpoC 765940 c.2571A>C synonymous_variant 0.15 rifampicin
rpoC 767034 p.Ser1222Leu missense_variant 0.12 rifampicin
rpoC 767144 p.Pro1259Thr missense_variant 0.17 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 775713 p.Ser923Leu missense_variant 0.12 clofazimine
bedaquiline
mmpL5 776055 p.Val809Gly missense_variant 0.11 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776190 p.Met764Arg missense_variant 0.18 clofazimine
bedaquiline
mmpL5 776432 c.2049G>A synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 776606 c.1875G>A synonymous_variant 0.14 clofazimine
bedaquiline
mmpL5 777158 c.1323C>A synonymous_variant 0.14 clofazimine
bedaquiline
mmpL5 777351 c.1129_1130insA frameshift_variant 0.18 clofazimine
bedaquiline
mmpL5 777868 p.Gln205* stop_gained 0.2 clofazimine
bedaquiline
mmpL5 778165 p.His106Asn missense_variant 0.21 clofazimine
bedaquiline
mmpR5 778211 c.-779C>T upstream_gene_variant 0.2 clofazimine
bedaquiline
mmpL5 778248 p.Ile78Ser missense_variant 0.18 clofazimine
bedaquiline
mmpS5 778890 p.Lys6Glu missense_variant 0.13 clofazimine
bedaquiline
mmpL5 778912 c.-432G>A upstream_gene_variant 0.17 clofazimine
bedaquiline
mmpS5 779539 c.-634C>A upstream_gene_variant 0.18 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
mmpS5 779633 c.-728T>G upstream_gene_variant 0.17 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781733 c.174G>A synonymous_variant 0.14 streptomycin
fbiC 1304502 c.1572G>A synonymous_variant 0.18 delamanid
fbiC 1304564 p.Thr545Ile missense_variant 0.18 delamanid
fbiC 1304617 p.Arg563Trp missense_variant 0.15 delamanid
fbiC 1305356 p.Gly809Val missense_variant 0.15 delamanid
Rv1258c 1406466 p.Ser292Trp missense_variant 0.17 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406854 p.Leu163Val missense_variant 0.18 streptomycin
pyrazinamide
isoniazid
embR 1416721 c.627A>C synonymous_variant 0.17 ethambutol
embR 1417268 p.Pro27Gln missense_variant 0.14 ethambutol
embR 1417316 p.Leu11Arg missense_variant 0.12 ethambutol Uncertain significance
embR 1417505 c.-158G>T upstream_gene_variant 0.11 ethambutol
atpE 1460946 c.-99A>C upstream_gene_variant 0.18 bedaquiline
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472657 n.812G>T non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.2 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.2 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.27 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.18 linezolid
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
aminoglycosides
streptomycin
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472892 n.1047T>G non_coding_transcript_exon_variant 0.14 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473172 n.1327T>A non_coding_transcript_exon_variant 0.13 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473908 n.251C>A non_coding_transcript_exon_variant 0.15 linezolid
rrl 1474174 n.517A>C non_coding_transcript_exon_variant 0.11 linezolid
rrl 1474929 n.1272A>C non_coding_transcript_exon_variant 0.14 linezolid
rrl 1474937 n.1280C>T non_coding_transcript_exon_variant 0.13 linezolid
rrl 1475273 n.1616T>G non_coding_transcript_exon_variant 0.14 linezolid
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.17 linezolid
rrl 1476781 n.3124C>A non_coding_transcript_exon_variant 0.14 linezolid
inhA 1673967 c.-235G>A upstream_gene_variant 0.11 ethionamide Uncertain significance
isoniazid
inhA 1674251 p.Thr17Ile missense_variant 0.11 ethionamide
isoniazid
inhA 1674781 p.Ile194Leu missense_variant 0.13 ethionamide
isoniazid
inhA 1674785 p.Arg195Leu missense_variant 0.13 ethionamide
isoniazid
rpsA 1833531 c.-11A>C upstream_gene_variant 0.11 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
ndh 2101747 c.1296C>T synonymous_variant 0.2 ethionamide
isoniazid
ndh 2101818 p.Thr409Pro missense_variant 0.11 ethionamide
isoniazid
ndh 2102518 c.525T>G synonymous_variant 0.13 ethionamide
isoniazid
ndh 2103079 c.-37T>G upstream_gene_variant 0.13 ethionamide
isoniazid
katG 2154116 p.Ile666Leu missense_variant 0.17 isoniazid
katG 2154214 p.Val633Gly missense_variant 0.13 isoniazid
katG 2154712 p.Leu467Trp missense_variant 0.14 isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2155540 p.Trp191Leu missense_variant 0.18 isoniazid
katG 2156185 c.-74T>G upstream_gene_variant 0.1 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2167934 c.2679G>A synonymous_variant 0.11 pyrazinamide
PPE35 2168051 c.2562G>T synonymous_variant 0.11 pyrazinamide
PPE35 2168943 p.Gln557Pro missense_variant 0.11 pyrazinamide
Rv1979c 2222510 p.Ser219Ala missense_variant 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222513 p.Phe218Val missense_variant 0.14 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289151 p.Ile31Leu missense_variant 0.12 pyrazinamide
pncA 2290220 c.-979G>T upstream_gene_variant 0.12 pyrazinamide
kasA 2517925 c.-190A>C upstream_gene_variant 0.12 isoniazid
kasA 2518138 p.Asn8Lys missense_variant 0.12 isoniazid
eis 2715161 p.Val58Leu missense_variant 0.12 kanamycin
amikacin
ahpC 2726226 p.Ala12Thr missense_variant 0.1 isoniazid
ahpC 2726521 p.Met110Arg missense_variant 0.18 isoniazid
ahpC 2726524 p.Leu111Pro missense_variant 0.2 isoniazid
folC 2746968 p.Gly211Arg missense_variant 0.12 para-aminosalicylic_acid
pepQ 2859474 c.945A>T synonymous_variant 0.14 clofazimine
bedaquiline
pepQ 2859575 p.Ala282Thr missense_variant 0.12 clofazimine
bedaquiline
Rv2752c 3065292 c.900T>G synonymous_variant 0.17 rifampicin
isoniazid
thyX 3067666 p.Ile94Val missense_variant 0.12 para-aminosalicylic_acid
thyX 3067839 p.Val36Gly missense_variant 0.11 para-aminosalicylic_acid
thyX 3068140 c.-195A>G upstream_gene_variant 0.12 para-aminosalicylic_acid
thyA 3073682 c.790T>A stop_lost&splice_region_variant 0.18 para-aminosalicylic_acid
thyA 3074399 p.Gly25* stop_gained 0.2 para-aminosalicylic_acid
thyA 3074445 c.27C>T synonymous_variant 0.2 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087487 p.Tyr223Cys missense_variant 0.18 cycloserine
Rv3083 3448568 p.His22Pro missense_variant 0.2 ethionamide
Rv3083 3448639 p.Asp46Tyr missense_variant 0.18 ethionamide
Rv3083 3449077 p.Leu192Val missense_variant 0.18 ethionamide
Rv3083 3449476 p.Thr325Pro missense_variant 0.11 ethionamide
Rv3083 3449555 p.Gln351Leu missense_variant 0.2 ethionamide
Rv3083 3449569 p.Met356Leu missense_variant 0.15 ethionamide
Rv3083 3449578 p.Ile359Val missense_variant 0.17 ethionamide
Rv3083 3449610 p.Glu369Asp missense_variant 0.15 ethionamide
Rv3083 3449654 p.Leu384Arg missense_variant 0.13 ethionamide
Rv3083 3449659 p.Trp386Arg missense_variant 0.17 ethionamide
Rv3083 3449677 p.Asn392Asp missense_variant 0.21 ethionamide
Rv3083 3449918 p.Ile472Ser missense_variant 0.2 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474414 c.408A>C synonymous_variant 0.18 capreomycin
amikacin
fprA 3474838 c.832_833insGG frameshift_variant 0.14 capreomycin
amikacin
fprA 3475046 p.Arg347Leu missense_variant 0.17 capreomycin
amikacin
whiB7 3568863 c.-184A>C upstream_gene_variant 0.14 streptomycin
kanamycin
amikacin
fbiB 3640881 c.-654G>T upstream_gene_variant 0.12 delamanid
fbiA 3641045 p.His168Pro missense_variant 0.13 delamanid
alr 3840357 p.Leu355Arg missense_variant 0.13 cycloserine
alr 3840373 p.Leu350Met missense_variant 0.12 cycloserine
alr 3840531 p.His297Pro missense_variant 0.17 cycloserine
rpoA 3878334 c.174T>G synonymous_variant 0.12 rifampicin
ddn 3986831 c.-13T>G upstream_gene_variant 0.17 delamanid
clpC1 4038688 p.Ile673Leu missense_variant 0.2 pyrazinamide
clpC1 4039468 p.Arg413Cys missense_variant 0.18 pyrazinamide
clpC1 4039596 p.His370Pro missense_variant 0.11 pyrazinamide
clpC1 4039647 p.Glu353Ala missense_variant 0.14 pyrazinamide
clpC1 4040569 p.Ala46Thr missense_variant 0.18 pyrazinamide
embC 4239814 c.-49A>C upstream_gene_variant 0.12 ethambutol
embC 4240722 p.Val287Gly missense_variant 0.15 ethambutol
embC 4241277 c.1417delG frameshift_variant 0.14 ethambutol
embC 4241337 p.Thr492Asn missense_variant 0.12 ethambutol Uncertain significance
embC 4241595 p.Ala578Glu missense_variant 0.18 ethambutol
embC 4241890 c.2028G>A synonymous_variant 0.11 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
embA 4244027 p.His265Gln missense_variant 0.12 ethambutol
embA 4245136 p.Tyr635Ser missense_variant 0.14 ethambutol
embA 4245322 p.Met697Arg missense_variant 0.11 ethambutol
embA 4245952 p.Pro907Gln missense_variant 0.2 ethambutol
embB 4248100 c.1587C>T synonymous_variant 0.14 ethambutol
embB 4248902 p.Thr797Pro missense_variant 0.2 ethambutol Uncertain significance
embB 4249577 p.Lys1022Gln missense_variant 0.2 ethambutol
aftB 4267423 c.1413dupG frameshift_variant 0.17 capreomycin
amikacin
aftB 4267495 p.Gly448Arg missense_variant 0.13 capreomycin
amikacin
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
aftB 4268001 p.Leu279Arg missense_variant 0.18 capreomycin
amikacin
ubiA 4269229 p.Thr202Ile missense_variant 0.23 ethambutol
ubiA 4269656 p.Val60Met missense_variant 0.14 ethambutol
ethA 4326561 p.Ile305Leu missense_variant 0.13 ethionamide
ethA 4327125 p.Thr117Pro missense_variant 0.15 ethionamide Uncertain significance
ethR 4327700 p.Ala51Asp missense_variant 0.13 ethionamide
ethR 4327739 p.Tyr64Ser missense_variant 0.14 ethionamide
ethA 4327755 c.-282T>C upstream_gene_variant 0.13 ethionamide
ethR 4327768 p.Thr74Pro missense_variant 0.14 ethionamide
whiB6 4338582 c.-61G>A upstream_gene_variant 0.12 streptomycin
capreomycin
amikacin
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
gid 4407787 p.Val139Ala missense_variant 0.11 streptomycin Uncertain significance
gid 4407808 p.Asp132Val missense_variant 0.1 streptomycin
gid 4407868 p.Val112Gly missense_variant 0.1 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance