TB-Profiler result

Run: SRR13861629
Summary

Run ID: SRR13861629

Sample name:

Date: 2024-10-05T07:38:17.415869

Number of reads: 709083

Percentage reads mapped: 14.2

Median coverage: 23.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
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 5149 c.-91G>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7090 p.Asp617Glu missense_variant 0.86 levofloxacin
moxifloxacin
gyrA 8436 p.Tyr379Asn missense_variant 0.96 levofloxacin
moxifloxacin
fgd1 491701 p.His307Asn missense_variant 1.0 pretomanid
delamanid
clofazimine
ccsA 619765 c.-126G>A upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
hadA 731718 c.-212T>C upstream_gene_variant 1.0 isoniazid
rpoB 760235 c.429T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.23 rifampicin
mmpL5 775867 p.Arg872Gly missense_variant 0.94 bedaquiline
clofazimine
mmpL5 776710 p.Cys591Ser missense_variant 1.0 bedaquiline
clofazimine
mmpL5 777625 p.Gln286Lys missense_variant 1.0 bedaquiline
clofazimine
mmpS5 778811 p.Phe32Ser missense_variant 1.0 bedaquiline
clofazimine
embR 1416901 c.447G>C synonymous_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.27 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.29 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.32 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474466 n.810delA non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1475224 n.1567T>C non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.76 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
bacA 2063516 p.Val405Ile missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2170487 c.126T>A synonymous_variant 0.95 pyrazinamide
Rv1979c 2221853 p.Phe438Ile missense_variant 1.0 bedaquiline
clofazimine
Rv2477c 2783563 c.480A>G synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783569 c.474C>G synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783572 c.471A>G synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783578 p.Glu155Asp missense_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783586 p.Ala153Pro missense_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783593 c.450T>C synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783596 c.447C>T synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783611 c.432C>G synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783629 c.414C>T synonymous_variant 0.27 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783641 c.402G>C synonymous_variant 0.31 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ribD 2987369 c.531G>A synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3073975 p.Arg166Pro missense_variant 0.93 para-aminosalicylic_acid
Rv3236c 3612013 c.1104A>T synonymous_variant 1.0 pyrazinamide
Rv3236c 3612032 p.Met362Arg missense_variant 1.0 pyrazinamide
Rv3236c 3613624 c.-508T>A upstream_gene_variant 1.0 pyrazinamide
lpqB 3625602 c.-692T>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3625616 p.Arg333Ala missense_variant 0.15 rifampicin
bedaquiline
lpqB 3625624 c.-714C>G upstream_gene_variant 0.19 rifampicin
bedaquiline
lpqB 3625627 c.-717C>T upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrB 3625654 c.959delT frameshift_variant 1.0 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3627491 c.-878G>T upstream_gene_variant 1.0 rifampicin
bedaquiline
rpoA 3878271 c.237T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
clpC1 4038498 p.Ser736Thr missense_variant 0.2 pyrazinamide
clpC1 4038536 c.2169C>T synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4039412 c.1293T>G synonymous_variant 0.2 pyrazinamide
embC 4240425 p.Arg188Pro missense_variant 1.0 ethambutol
embC 4240477 c.615C>A synonymous_variant 1.0 ethambutol
embC 4240678 c.816T>G synonymous_variant 0.18 ethambutol
embC 4240685 p.Thr275Ala missense_variant 0.2 ethambutol
embC 4240693 c.831T>C synonymous_variant 0.19 ethambutol
embA 4244214 p.Ala328Ser missense_variant 1.0 ethambutol
embA 4244849 c.1617C>G synonymous_variant 1.0 ethambutol
embB 4247198 p.Thr229Pro missense_variant 1.0 ethambutol
embB 4247381 p.Trp290Arg missense_variant 1.0 ethambutol
aftB 4268115 p.Leu241Arg missense_variant 1.0 ethambutol
aftB 4268696 c.141G>A synonymous_variant 1.0 ethambutol
ethA 4326298 c.1176G>A synonymous_variant 0.94 ethionamide
whiB6 4338567 c.-46C>A upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance