TB-Profiler result

Run: DRR184617
Summary

Run ID: DRR184617

Sample name:

Date: 2024-03-24T18:10:25.761323

Number of reads: 11547781

Percentage reads mapped: 84.92

Median coverage: 364.0

Strain: lineage2.2.1.1

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
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 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.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
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
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 761311 p.Pro502Leu missense_variant 1.0 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476229 n.2572C>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476269 n.2612C>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476274 n.2617G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 1.0 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
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
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244744 c.1512C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248115 c.1602C>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 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
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