TB-Profiler result

Run: SRR13861644

Summary

Run ID: SRR13861644

Sample name:

Date: 2024-04-15T02:58:47.600111

Number of reads: 1035330

Percentage reads mapped: 51.82

Median coverage: 35.0

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 6624 p.Ser462* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin
gyrA 7285 c.-17T>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 8798 c.1497C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rpoC 764438 c.1069_1070insA frameshift_variant 1.0 rifampicin
mmpL5 775795 p.Ala896Ser missense_variant 1.0 clofazimine
bedaquiline
fbiC 1303593 c.663G>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
embR 1416428 c.919_920insT frameshift_variant 1.0 ethambutol Uncertain significance
rrs 1471798 n.-48G>A upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472913 n.1068G>C non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476167 n.2510T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674226 p.Arg9Trp missense_variant 1.0 ethionamide
isoniazid
rpsA 1833352 c.-190C>A upstream_gene_variant 1.0 pyrazinamide
rpsA 1833710 p.Tyr57Asp missense_variant 1.0 pyrazinamide
rpsA 1834711 c.1170C>T synonymous_variant 1.0 pyrazinamide
ndh 2102326 c.717G>T synonymous_variant 1.0 ethionamide
delamanid
isoniazid
Rv1979c 2222739 c.426C>A synonymous_variant 1.0 clofazimine
bedaquiline
Rv1979c 2222936 p.Ala77Thr missense_variant 1.0 clofazimine
bedaquiline
eis 2714217 c.1115dupC frameshift_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2714361 c.972C>A synonymous_variant 1.0 amikacin
kanamycin
ahpC 2725906 c.-287C>G upstream_gene_variant 1.0 isoniazid
Rv2477c 2782975 c.1068C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
pepQ 2859813 p.Ile202Met missense_variant 1.0 clofazimine
bedaquiline
pepQ 2860286 p.Val45Leu missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ribD 2987503 p.Gly222Val missense_variant 1.0 para-aminosalicylic_acid
ald 3087394 p.Ala192Val missense_variant 0.97 cycloserine
ald 3087464 c.645C>T synonymous_variant 1.0 cycloserine
ald 3087512 c.693T>A synonymous_variant 1.0 cycloserine
Rv3083 3448303 c.-201G>C upstream_gene_variant 1.0 ethionamide
lpqB 3623311 p.Pro534Ser missense_variant 1.0 bedaquiline
rifampicin
lpqB 3623400 p.Val504Glu missense_variant 1.0 bedaquiline
rifampicin
lpqB 3624438 p.Gln158Leu missense_variant 1.0 bedaquiline
rifampicin
rpoA 3879111 c.-604G>C upstream_gene_variant 1.0 rifampicin
embC 4241874 p.Leu671Arg missense_variant 1.0 ethambutol
embC 4242816 p.Trp985* stop_gained 1.0 ethambutol
embB 4248365 p.Val618Met missense_variant 1.0 ethambutol Uncertain significance
aftB 4267893 p.Ile315Ser missense_variant 1.0 ethambutol
aftB 4268516 c.321A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethR 4326691 c.-858C>A upstream_gene_variant 1.0 ethionamide