TB-Profiler result

Run: SRR13861605
Summary

Run ID: SRR13861605

Sample name:

Date: 2024-10-05T00:54:38.712826

Number of reads: 1507627

Percentage reads mapped: 30.18

Median coverage: 50.0

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 5785 c.546C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrB 6314 c.1076dupC frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
gyrA 7495 p.Arg65His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8780 p.Asp493Glu missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13273 p.Gly96Cys missense_variant 1.0 isoniazid
Rv0010c 13363 p.Asp66Tyr missense_variant 1.0 isoniazid
mshA 574744 c.-604G>A upstream_gene_variant 1.0 isoniazid
ethionamide
ccsA 620129 p.Gly80Ala missense_variant 1.0 kanamycin
capreomycin
amikacin
rpoB 761845 p.Gln680Arg missense_variant 1.0 rifampicin
rpsL 781185 c.-375T>G upstream_gene_variant 1.0 streptomycin
rpsL 781226 c.-334C>T upstream_gene_variant 1.0 streptomycin
rplC 800937 c.129A>G synonymous_variant 1.0 linezolid
embR 1416298 c.1050G>C synonymous_variant 1.0 ethambutol
embR 1417588 c.-241C>T upstream_gene_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.22 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.22 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
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475592 n.1935A>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.56 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 0.56 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1918324 p.Val129Leu missense_variant 1.0 capreomycin
bacA 2064860 c.-132A>G upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2168503 p.Phe704Leu missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670His missense_variant 1.0 pyrazinamide
Rv1979c 2223395 c.-231G>T upstream_gene_variant 1.0 bedaquiline
clofazimine
ahpC 2726771 c.579T>A synonymous_variant 1.0 isoniazid
folC 2746808 p.Ala264Gly missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3067057 c.-867_-866insG upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3087587 c.769delC frameshift_variant 1.0 cycloserine
lpqB 3624686 p.Glu75Asp missense_variant 1.0 rifampicin
bedaquiline
fbiA 3641252 p.Thr237Ser missense_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3877496 p.Glu338* stop_gained 1.0 rifampicin
ddn 3986684 c.-160G>C upstream_gene_variant 1.0 pretomanid
delamanid
embC 4238901 c.-962T>A upstream_gene_variant 1.0 ethambutol
embC 4240480 c.618G>A synonymous_variant 1.0 ethambutol
embA 4244410 p.Trp393Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4249447 c.2934G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338681 c.-160A>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin