TB-Profiler result

Run: SAMN02360583
Summary

Run ID: SAMN02360583

Sample name:

Date: 2025-02-27T10:29:46.937375

Number of reads: 1080685

Percentage reads mapped: 6.97

Median coverage: 24.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.99
lineage2.2 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 katG p.Ser140Asn Uncertain significance Mutation from literature
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
katG 2155693 p.Ser140Asn missense_variant 0.78 isoniazid Uncertain significance Mutation from literature
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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760752 c.946C>T synonymous_variant 1.0 rifampicin Uncertain significance
rpoB 762881 p.Met1025Ile missense_variant 0.23 rifampicin Uncertain significance
rpoC 762893 c.-477C>T upstream_gene_variant 0.59 rifampicin Uncertain significance
rpoC 762896 c.-474G>C upstream_gene_variant 0.62 rifampicin Uncertain significance
rpoB 762917 c.3111C>G synonymous_variant 0.72 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.68 rifampicin Uncertain significance
rpoB 762929 c.3123G>T synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.65 rifampicin Uncertain significance
rpoB 762942 p.Ile1046Val missense_variant 0.65 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.69 rifampicin Uncertain significance
rpoC 762980 c.-390T>C upstream_gene_variant 0.62 rifampicin Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.52 rifampicin Uncertain significance
rpoB 762995 c.3189G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 762998 c.-372G>A upstream_gene_variant 0.32 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 764329 c.960C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764338 p.Glu323Asp missense_variant 0.56 rifampicin Uncertain significance
rpoC 764344 c.975C>T synonymous_variant 0.57 rifampicin Uncertain significance
rpoC 764348 p.Met327Leu missense_variant 0.59 rifampicin Uncertain significance
rpoC 764355 p.Gln329Pro missense_variant 0.62 rifampicin Uncertain significance
rpoC 764377 c.1008C>G synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.63 rifampicin Uncertain significance
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.63 rifampicin Uncertain significance
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>T synonymous_variant 0.62 rifampicin Uncertain significance
rpoC 764428 c.1059G>T synonymous_variant 0.54 rifampicin Uncertain significance
rpoC 764434 c.1065A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066A>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764443 p.Ile358Met missense_variant 0.24 rifampicin Uncertain significance
rpoC 764587 c.1218C>G synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 764593 c.1224C>T synonymous_variant 0.21 rifampicin Uncertain significance
rpoC 764611 c.1242G>C synonymous_variant 0.21 rifampicin Uncertain significance
rpoC 764632 c.1263T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 778656 p.Ala84Thr missense_variant 0.91 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1303856 p.Ala309Val missense_variant 0.95 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.46 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.67 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.67 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.66 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.65 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.66 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.6 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.62 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.59 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.54 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.56 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.46 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.39 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.43 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.41 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.36 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.37 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.36 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.37 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.39 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.39 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.42 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.63 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.63 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.65 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.68 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.61 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.51 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.53 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.66 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.66 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.7 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.7 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.71 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.69 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.68 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.67 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833909 p.Asp123Ala missense_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155572 c.540G>C synonymous_variant 0.27 isoniazid Uncertain significance
katG 2155600 p.Cys171Val missense_variant 0.55 isoniazid Uncertain significance
katG 2155613 p.Phe167Leu missense_variant 0.56 isoniazid Uncertain significance
katG 2155614 c.498T>C synonymous_variant 0.56 isoniazid Uncertain significance
katG 2155617 p.Ile165Met missense_variant 0.59 isoniazid Uncertain significance
katG 2155626 c.486G>C synonymous_variant 0.63 isoniazid Uncertain significance
katG 2155637 p.Leu159Ile missense_variant 0.66 isoniazid Uncertain significance
katG 2155641 p.Lys157Arg missense_variant 0.66 isoniazid Uncertain significance
katG 2155650 c.462G>A synonymous_variant 0.72 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.72 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.75 isoniazid Uncertain significance
katG 2155668 c.444G>C synonymous_variant 0.76 isoniazid Uncertain significance
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.78 isoniazid Not assoc w R - Interim
katG 2155704 c.408C>T synonymous_variant 0.81 isoniazid Uncertain significance
katG 2155716 c.396T>C synonymous_variant 0.78 isoniazid Uncertain significance
katG 2155722 c.390G>C synonymous_variant 0.76 isoniazid Uncertain significance
katG 2155728 c.384G>C synonymous_variant 0.74 isoniazid Uncertain significance
katG 2155735 p.Met126Gln missense_variant 0.69 isoniazid Uncertain significance
katG 2155737 c.375C>T synonymous_variant 0.69 isoniazid Uncertain significance
katG 2155741 p.Gly124Ala missense_variant 0.66 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.66 isoniazid Uncertain significance
katG 2155765 p.His116Thr missense_variant 0.48 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3987084 p.Gly81Ser missense_variant 1.0 delamanid Uncertain significance
pretomanid Uncertain significance
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R