TB-Profiler result

Run: 4af9f384-4f1e-4ccd-8859-a78f03521ab9
Summary

Run ID: 4af9f384-4f1e-4ccd-8859-a78f03521ab9

Sample name:

Date: 24-11-2023 05:12:37

Number of reads: 695320

Percentage reads mapped: 77.56

Median coverage: 21

Strain: lineage3.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 1.0
lineage3.1 East-African-Indian RD750 1.0
lineage3.1.2 East-African-Indian RD750 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
isoniazid
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
p.Asp1024Asn Uncertain significance
pyrazinamide pncA p.Trp68* Assoc w R - interim
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin tlyA c.413delG Uncertain significance
c.567dupA Uncertain significance
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
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin Assoc w R
tlyA 1918350 c.413delG frameshift_variant 0.16 capreomycin Uncertain significance
tlyA 1918503 c.567dupA frameshift_variant 0.3 capreomycin Uncertain significance
pncA 2289038 p.Trp68* stop_gained 0.8 pyrazinamide Assoc w R - interim
embB 4247429 p.Met306Val missense_variant 0.16 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.39 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 576005 c.660delA frameshift_variant 0.18 ethionamide
isoniazid
mshA 576170 p.Gln275Glu missense_variant 0.18 ethionamide
isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 762434 c.-936T>G upstream_gene_variant 1.0 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777024 c.1456delC frameshift_variant 0.27 clofazimine
bedaquiline
mmpL5 778042 c.438delC frameshift_variant 0.23 clofazimine
bedaquiline
mmpS5 778649 c.256delC frameshift_variant 0.21 clofazimine
bedaquiline
mmpS5 779597 c.-693delA upstream_gene_variant 0.32 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 801168 c.363delA frameshift_variant 0.18 linezolid
fbiC 1303096 c.168delC frameshift_variant 0.3 delamanid
embR 1416846 p.Glu168Lys missense_variant 0.11 ethambutol
embR 1416892 c.456C>T synonymous_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.12 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1475205 n.1551delC non_coding_transcript_exon_variant 0.32 linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14 linezolid
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12 linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15 linezolid
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.14 linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12 linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15 linezolid
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14 linezolid
rpsA 1833414 c.-127delT upstream_gene_variant 0.24 pyrazinamide
rpsA 1833778 c.238delG frameshift_variant 0.23 pyrazinamide
rpsA 1834955 c.1417delC frameshift_variant 0.25 pyrazinamide
rpsA 1834964 c.1428delA frameshift_variant 0.21 pyrazinamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2155076 c.997_1035dupCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAG conservative_inframe_insertion 0.3 isoniazid
katG 2156445 c.-335delC upstream_gene_variant 0.23 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.99 pyrazinamide Uncertain significance
PPE35 2169988 c.625T>C synonymous_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
pncA 2289585 c.-345dupT upstream_gene_variant 0.11 pyrazinamide
kasA 2518017 c.-98_-97insA upstream_gene_variant 0.11 isoniazid
ahpC 2726076 c.-116delT upstream_gene_variant 0.36 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
folC 2747201 p.Leu133Arg missense_variant 1.0 para-aminosalicylic_acid
folC 2747699 c.-102dupT upstream_gene_variant 0.18 para-aminosalicylic_acid
pepQ 2859414 c.1004delG frameshift_variant 0.3 clofazimine
bedaquiline
Rv2752c 3064594 c.1597delG frameshift_variant 0.15 rifampicin Uncertain significance
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339288 c.171C>T synonymous_variant 0.15 delamanid
Rv3083 3448882 c.382dupA frameshift_variant 0.14 ethionamide Uncertain significance
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fbiA 3640763 c.226delC frameshift_variant 0.21 delamanid
fbiB 3641598 c.66dupA frameshift_variant 0.14 delamanid
alr 3840314 c.1106delG frameshift_variant 0.25 cycloserine
alr 3841306 c.114delC frameshift_variant 0.19 cycloserine
rpoA 3877799 c.708delG frameshift_variant 0.12 rifampicin
rpoA 3878311 c.196delG frameshift_variant 0.13 rifampicin
ddn 3987251 p.Tyr136* stop_gained 0.12 delamanid
clpC1 4038911 c.1793delC frameshift_variant 0.19 pyrazinamide
embC 4240962 c.1104delG frameshift_variant 0.36 ethambutol
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Uncertain significance
embC 4242910 c.3050delG frameshift_variant 0.15 ethambutol
embB 4247182 c.673delG frameshift_variant 0.18 ethambutol
embB 4247581 c.1068C>T synonymous_variant 0.18 ethambutol
embB 4249535 c.3025dupA frameshift_variant 0.13 ethambutol
aftB 4267432 c.1404delC frameshift_variant 0.33 capreomycin
amikacin
ubiA 4269303 c.530dupT frameshift_variant 0.12 ethambutol
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 4407813 c.389delG frameshift_variant 0.43 streptomycin