TB-Profiler result

Run: SRR13861508
Summary

Run ID: SRR13861508

Sample name:

Date: 2024-10-04T22:11:38.525234

Number of reads: 824053

Percentage reads mapped: 16.5

Median coverage: 27.0

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
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.1301delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1304229 c.1301delC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 8880 p.Lys527Gln missense_variant 1.0 levofloxacin
moxifloxacin
mmaA3 737817 c.333A>G synonymous_variant 1.0 isoniazid
rpoB 760972 p.Arg389Leu missense_variant 1.0 rifampicin
rpoC 765111 p.Met581Lys missense_variant 1.0 rifampicin
rpoC 765161 p.Glu598Lys missense_variant 1.0 rifampicin
rpoC 765540 p.Ala724Val missense_variant 1.0 rifampicin
rpoC 767068 c.3699G>T synonymous_variant 1.0 rifampicin
mmpR5 778439 c.-551C>A upstream_gene_variant 1.0 bedaquiline
clofazimine
rplC 801357 p.His183Gln missense_variant 1.0 linezolid
rrs 1472288 n.444delT non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.81 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 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.77 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 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1853872 c.267G>T synonymous_variant 1.0 linezolid
tlyA 1917989 p.Ala17Gly missense_variant 1.0 capreomycin
bacA 2063805 c.924G>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
bacA 2064585 c.144C>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102525 p.Phe173Tyr missense_variant 1.0 isoniazid
delamanid
ethionamide
ndh 2102538 c.504_505insT frameshift_variant 1.0 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
Rv1979c 2222978 p.Ile63Phe missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223052 p.Glu38Val missense_variant 1.0 bedaquiline
clofazimine
pncA 2289415 c.-174C>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518057 c.-58A>C upstream_gene_variant 1.0 isoniazid
kasA 2518799 p.Pro229Ser missense_variant 1.0 isoniazid
eis 2714983 p.Ala117Glu missense_variant 1.0 kanamycin
amikacin
Rv2477c 2784409 c.-367T>A upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784611 c.-569A>T upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
fbiA 3640404 c.-139C>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3642056 c.522C>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3877967 p.Thr181Ser missense_variant 1.0 rifampicin Uncertain significance
rpoA 3877972 c.535delG frameshift_variant 1.0 rifampicin
clpC1 4039777 c.927_928insG frameshift_variant 1.0 pyrazinamide
glpK 4138934 c.822A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embB 4247545 p.Ser344Arg missense_variant 1.0 ethambutol Uncertain significance
aftB 4268812 p.Ser9Pro missense_variant 1.0 ethambutol