TB-Profiler result

Run: SRR13861719
Summary

Run ID: SRR13861719

Sample name:

Date: 2024-04-15T00:41:35.792695

Number of reads: 694574

Percentage reads mapped: 34.76

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
Rv0565c 657081 c.390G>C synonymous_variant 1.0 ethionamide
nusG 733855 c.-399G>A upstream_gene_variant 1.0 rifampicin
rpoB 759613 c.-194C>A upstream_gene_variant 1.0 rifampicin
rpoB 759854 p.Ser16Arg missense_variant 1.0 rifampicin
rpoC 765119 p.Gly584Arg missense_variant 1.0 rifampicin
rpoC 766845 p.Arg1159His missense_variant 1.0 rifampicin
mmpL5 776280 p.Arg734His missense_variant 1.0 clofazimine
bedaquiline
mmpR5 778208 c.-782C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
fbiC 1305195 c.2265T>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
Rv1258c 1406120 c.1221C>T synonymous_variant 1.0 streptomycin
isoniazid
pyrazinamide
embR 1417526 c.-180delA upstream_gene_variant 1.0 ethambutol
rrl 1473960 n.303T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833623 c.82_83insG frameshift_variant 1.0 pyrazinamide Uncertain significance
tlyA 1918515 c.576C>T synonymous_variant 1.0 capreomycin
tlyA 1918620 c.681C>A synonymous_variant 1.0 capreomycin
katG 2155055 p.Tyr353Asn missense_variant 1.0 isoniazid
PPE35 2169626 c.987C>T synonymous_variant 1.0 pyrazinamide
eis 2714776 p.Val186Glu missense_variant 1.0 amikacin
kanamycin
ahpC 2726084 c.-109C>A upstream_gene_variant 0.95 isoniazid
Rv2477c 2782646 c.1396delC frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3065052 p.Glu380Asp missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065097 c.1095C>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073902 c.570C>G synonymous_variant 1.0 para-aminosalicylic_acid
lpqB 3623705 c.1205dupA frameshift_variant 1.0 bedaquiline
rifampicin Uncertain significance
mtrB 3624963 p.Pro551Thr missense_variant 1.0 bedaquiline
rifampicin
panD 4044175 p.Ala36Asp missense_variant 1.0 pyrazinamide
embC 4240583 p.Thr241Ala missense_variant 1.0 ethambutol
whiB6 4338609 c.-88T>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407696 c.507C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim