TB-Profiler result

Run: SRR13861399
Summary

Run ID: SRR13861399

Sample name:

Date: 2024-10-05T07:38:08.323688

Number of reads: 1373768

Percentage reads mapped: 45.84

Median coverage: 47.0

Strain: 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 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 rrs n.462C>T Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.14 streptomycin 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
gyrB 6027 p.His263Arg missense_variant 1.0 levofloxacin
moxifloxacin
mshA 576327 p.Phe327Tyr missense_variant 1.0 isoniazid
ethionamide
ccsA 620307 c.417C>G synonymous_variant 0.15 kanamycin
capreomycin
amikacin
Rv0565c 656192 p.Asp427His missense_variant 1.0 ethionamide
rpoB 759707 c.-100C>T upstream_gene_variant 1.0 rifampicin
rpoB 760178 c.372G>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 760934 c.1128C>T synonymous_variant 0.16 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760970 c.1164G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.17 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.17 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>A synonymous_variant 1.0 rifampicin
rpoC 764262 p.Val298Ala missense_variant 0.94 rifampicin
rpoC 764389 p.Leu340Phe missense_variant 0.14 rifampicin Uncertain significance
rpoC 764431 c.1062G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.15 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.15 rifampicin
rpoC 764455 c.1086G>C synonymous_variant 0.15 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.14 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
mmpL5 777280 p.Ala401Ser missense_variant 1.0 bedaquiline
clofazimine
mmpS5 778853 p.Val18Ala missense_variant 1.0 bedaquiline
clofazimine
rpsL 781277 c.-283G>C upstream_gene_variant 1.0 streptomycin
rplC 800213 c.-596G>T upstream_gene_variant 1.0 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.15 linezolid
rplC 800794 c.-15_-9delAGATTGGinsGAGTT upstream_gene_variant 0.19 linezolid
rplC 800814 c.6A>G synonymous_variant 0.18 linezolid
rplC 800817 c.9A>T synonymous_variant 0.18 linezolid
rplC 800844 c.36T>C synonymous_variant 0.14 linezolid
rplC 800874 c.66A>G synonymous_variant 0.12 linezolid
embR 1416662 p.Arg229Pro missense_variant 1.0 ethambutol
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
tlyA 1917545 c.-395T>A upstream_gene_variant 1.0 capreomycin
katG 2155675 p.Arg146Leu missense_variant 0.89 isoniazid Uncertain significance
Rv1979c 2222433 c.732A>G synonymous_variant 1.0 bedaquiline
clofazimine
kasA 2518732 c.618C>G synonymous_variant 0.17 isoniazid
kasA 2518741 c.627G>C synonymous_variant 0.17 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.16 isoniazid
kasA 2518768 c.654C>G synonymous_variant 0.16 isoniazid
kasA 2518783 c.669T>C synonymous_variant 0.16 isoniazid
kasA 2518792 c.678C>G synonymous_variant 0.15 isoniazid
kasA 2518795 c.681C>G synonymous_variant 0.15 isoniazid
Rv2477c 2783883 c.160T>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2996147 p.Glu15Gln missense_variant 1.0 capreomycin
Rv2681 2996821 p.Gly28Val missense_variant 1.0 capreomycin
thyA 3073872 p.Ile200Val missense_variant 0.14 para-aminosalicylic_acid
thyA 3073878 c.594G>A synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073892 c.580T>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3073893 c.579C>G synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3073925 c.547T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073926 c.546G>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3073929 c.543T>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3074010 c.462C>G synonymous_variant 0.14 para-aminosalicylic_acid
ald 3086631 c.-189A>G upstream_gene_variant 1.0 cycloserine
Rv3236c 3612954 c.162delC frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613619 c.-503T>G upstream_gene_variant 1.0 pyrazinamide
alr 3840284 p.Trp379* stop_gained 0.97 cycloserine
rpoA 3877818 c.690A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.19 rifampicin
rpoA 3877866 c.642G>C synonymous_variant 0.17 rifampicin
rpoA 3877872 c.636C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877875 c.633T>G synonymous_variant 0.19 rifampicin
rpoA 3878924 c.-417G>C upstream_gene_variant 0.13 rifampicin
rpoA 3879040 c.-533G>C upstream_gene_variant 0.13 rifampicin
clpC1 4038347 c.2358G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038611 c.2094C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039073 c.1632C>G synonymous_variant 0.13 pyrazinamide
glpK 4139736 p.Gly7Val missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4239589 c.-273delA upstream_gene_variant 1.0 ethambutol
embC 4240042 p.Asn60Lys missense_variant 1.0 ethambutol
embC 4240936 c.1074A>G synonymous_variant 0.15 ethambutol
embB 4245806 c.-708G>A upstream_gene_variant 0.96 ethambutol
embB 4247075 c.563dupT frameshift_variant 1.0 ethambutol
embB 4247839 c.1326G>A synonymous_variant 0.96 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.13 ethambutol
embB 4248118 c.1605T>C synonymous_variant 0.16 ethambutol
embB 4248127 c.1614G>C synonymous_variant 0.16 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.16 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.17 ethambutol
embB 4248143 c.1630T>C synonymous_variant 0.17 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.19 ethambutol Not assoc w R - Interim
embB 4249763 p.Thr1084Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4326860 p.Leu205Pro missense_variant 1.0 ethionamide Uncertain significance