TB-Profiler result

Run: SRR13861560
Summary

Run ID: SRR13861560

Sample name:

Date: 2024-04-14T10:51:56.309295

Number of reads: 586893

Percentage reads mapped: 14.69

Median coverage: 19.0

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
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.905delT Assoc w R
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
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide Assoc w R
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 8820 p.Asp507His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575967 p.Val207Asp missense_variant 1.0 ethionamide
isoniazid
rpoB 759961 p.Thr52Asn missense_variant 1.0 rifampicin
rpoB 763050 p.Leu1082Met missense_variant 1.0 rifampicin
mmpL5 775701 p.Pro927Gln missense_variant 1.0 clofazimine
bedaquiline
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 800500 c.-309A>C upstream_gene_variant 1.0 linezolid
rplC 801353 p.Val182Ala missense_variant 1.0 linezolid
Rv1129c 1253966 p.Leu190Trp missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1304512 p.Val528Ile missense_variant 1.0 clofazimine
pretomanid
delamanid
embR 1417704 c.-357T>C upstream_gene_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68 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
rpsA 1834175 p.Arg212* stop_gained 1.0 pyrazinamide Uncertain significance
katG 2156840 c.-729C>T upstream_gene_variant 1.0 isoniazid
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0 clofazimine
bedaquiline
ald 3087218 p.Met133Ile missense_variant 1.0 cycloserine
whiB7 3568679 p.Val1Leu missense_variant 1.0 streptomycin
amikacin
kanamycin
whiB7 3568989 c.-310A>C upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
mtrB 3625440 p.Gly392Arg missense_variant 1.0 bedaquiline
rifampicin
clpC1 4040066 c.639G>T synonymous_variant 1.0 pyrazinamide
embC 4241259 c.1397_1398insT frameshift_variant 1.0 ethambutol
embA 4243358 c.126C>T synonymous_variant 1.0 ethambutol
embA 4243469 c.237C>T synonymous_variant 1.0 ethambutol
embB 4248436 c.1923C>T synonymous_variant 1.0 ethambutol
ubiA 4269557 p.Ala93Pro missense_variant 1.0 ethambutol