TB-Profiler result

Run: SRR13861151
Summary

Run ID: SRR13861151

Sample name:

Date: 2024-10-04T22:11:19.046610

Number of reads: 739881

Percentage reads mapped: 12.34

Median coverage: 24.0

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
gyrA 9502 p.Arg734His missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13527 p.Ser11* stop_gained 1.0 isoniazid Uncertain significance
rpoB 759681 c.-126C>T upstream_gene_variant 0.95 rifampicin
rpoB 761239 p.Cys478Tyr missense_variant 0.68 rifampicin
rpoC 764530 c.1161C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
mmpL5 776185 p.Lys766Glu missense_variant 1.0 bedaquiline
clofazimine
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0 bedaquiline
clofazimine
embR 1417986 c.-639T>A upstream_gene_variant 1.0 ethambutol
rrs 1472865 n.1020C>G non_coding_transcript_exon_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.37 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 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
tlyA 1918063 p.Pro42Ala missense_variant 1.0 capreomycin
ndh 2102985 p.Ile20Val missense_variant 1.0 isoniazid
delamanid
ethionamide
katG 2155856 p.Thr86Ser missense_variant 1.0 isoniazid
PPE35 2169233 c.1379delT frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv2477c 2783395 c.648T>C synonymous_variant 0.28 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3065376 c.815delT frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066351 c.-160G>T upstream_gene_variant 0.94 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067731 p.Val72Ala missense_variant 0.94 para-aminosalicylic_acid
thyX 3067825 p.Arg41Gly missense_variant 1.0 para-aminosalicylic_acid
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
Rv3083 3448707 c.204G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3449768 p.Thr422Lys missense_variant 1.0 ethionamide
lpqB 3623219 c.1692A>G synonymous_variant 1.0 rifampicin
bedaquiline
mtrA 3627790 c.-441A>G upstream_gene_variant 1.0 rifampicin
bedaquiline
fbiB 3641403 c.-132C>T upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
alr 3841257 p.His55Leu missense_variant 1.0 cycloserine
rpoA 3877601 p.Gln303* stop_gained 0.96 rifampicin
ddn 3986668 c.-176T>C upstream_gene_variant 1.0 pretomanid
delamanid
embC 4239401 c.-462A>C upstream_gene_variant 1.0 ethambutol
embC 4241864 p.Leu668Met missense_variant 1.0 ethambutol
embB 4245557 c.-957G>A upstream_gene_variant 1.0 ethambutol
ethA 4327092 p.Ala128Pro missense_variant 1.0 ethionamide
gid 4408151 p.Leu18Val missense_variant 1.0 streptomycin