TB-Profiler result

Run: SRR13861620

Summary

Run ID: SRR13861620

Sample name:

Date: 2024-10-05T06:19:01.272903

Number of reads: 1950026

Percentage reads mapped: 39.04

Median coverage: 66.0

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
dnaA 1427 p.Ala476Gly missense_variant 1.0 isoniazid
gyrA 7346 p.Ile15Met missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 8335 p.Met345Arg missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9639 p.Gly780Arg missense_variant 1.0 levofloxacin
moxifloxacin
fgd1 491505 c.723G>A synonymous_variant 1.0 pretomanid
delamanid
clofazimine
mshA 576310 p.Ile321Met missense_variant 1.0 isoniazid
ethionamide
Rv0565c 657451 p.Ala7Val missense_variant 1.0 ethionamide
mmpL5 775981 p.Leu834Val missense_variant 1.0 bedaquiline
clofazimine
mmpL5 776732 c.1749C>T synonymous_variant 1.0 bedaquiline
clofazimine
mmpL5 777942 p.Pro180Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800343 c.-466G>C upstream_gene_variant 1.0 linezolid
fbiC 1303422 c.492A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1406592 p.Tyr250Cys missense_variant 1.0 streptomycin
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416737 p.Arg204Gln missense_variant 1.0 ethambutol
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834091 p.Val184Met missense_variant 1.0 pyrazinamide
tlyA 1918473 c.534T>A synonymous_variant 1.0 capreomycin
Rv1979c 2221849 p.Leu439Gln missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222231 p.Met312Leu missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222710 p.Asn152Ile missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223809 c.-646_-645insT upstream_gene_variant 1.0 bedaquiline
clofazimine
eis 2714723 p.Cys204Gly missense_variant 1.0 kanamycin
amikacin
folC 2746975 p.Asp208Glu missense_variant 0.99 para-aminosalicylic_acid
Rv2477c 2782420 c.1623T>A synonymous_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784310 c.-268T>A upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2860233 c.186T>G synonymous_variant 1.0 bedaquiline
clofazimine
thyA 3073781 p.Leu231Ile missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448420 c.-84_-83insT upstream_gene_variant 1.0 ethionamide
whiB7 3568689 c.-11delT upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
embC 4240494 p.Gly211Ala missense_variant 1.0 ethambutol Uncertain significance
embC 4241732 p.Ala624Pro missense_variant 1.0 ethambutol
embA 4245672 p.Gly814Arg missense_variant 1.0 ethambutol
embB 4247458 p.Tyr315* stop_gained 1.0 ethambutol
aftB 4268265 p.Leu191Gln missense_variant 1.0 ethambutol