TB-Profiler result

Run: SRR13861528

Summary

Run ID: SRR13861528

Sample name:

Date: 2024-10-05T06:18:58.066443

Number of reads: 645150

Percentage reads mapped: 64.58

Median coverage: 22.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB


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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 katG c.1700delT Assoc w R High-level resistance
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
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid Assoc w R High-level 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 7949 c.648G>T synonymous_variant 0.93 levofloxacin
moxifloxacin
gyrA 8123 p.Leu274Phe missense_variant 0.88 levofloxacin Uncertain significance
moxifloxacin
gyrA 9768 p.Gly823Cys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 657349 p.Glu41Val missense_variant 0.96 ethionamide
mmaA3 738066 c.84C>T synonymous_variant 1.0 isoniazid
rpoC 763441 c.72C>G synonymous_variant 0.3 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 763734 p.Pro122Leu missense_variant 0.89 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.24 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.28 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Gln missense_variant 0.31 rifampicin
rpoC 764203 c.834G>T synonymous_variant 0.33 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764320 c.951C>G synonymous_variant 0.22 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.28 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpsL 781892 c.333A>G synonymous_variant 0.21 streptomycin
Rv1129c 1253309 p.His409Pro missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
tsnR 1853566 c.-40C>T upstream_gene_variant 1.0 linezolid
tlyA 1918034 p.Val32Ala missense_variant 1.0 capreomycin
bacA 2064615 p.Leu38Phe missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
katG 2155918 p.Ala65Val missense_variant 1.0 isoniazid
PPE35 2168767 p.Ser616Gly missense_variant 1.0 pyrazinamide
PPE35 2170815 c.-203C>G upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2222377 p.Val263Gly missense_variant 1.0 bedaquiline
clofazimine
kasA 2518723 p.Glu203Asp missense_variant 0.22 isoniazid
kasA 2518732 c.618C>G synonymous_variant 0.24 isoniazid
kasA 2518768 c.654C>G synonymous_variant 0.23 isoniazid
Rv2477c 2783104 c.939C>A synonymous_variant 0.92 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.27 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783794 c.249G>A synonymous_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783797 p.Asp82Glu missense_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783815 c.228A>G synonymous_variant 0.27 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783833 c.210G>C synonymous_variant 0.28 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.25 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783860 p.Asp61Glu missense_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.19 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ribD 2986993 p.Gly52Val missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3065787 c.405G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066807 c.-616T>C upstream_gene_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066813 c.-622C>T upstream_gene_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066819 c.-628T>C upstream_gene_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066822 c.-631T>C upstream_gene_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066839 c.-648A>G upstream_gene_variant 0.19 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448649 p.Arg49Pro missense_variant 1.0 ethionamide
Rv3236c 3613067 p.Val17Gly missense_variant 1.0 pyrazinamide
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0 pyrazinamide
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3878982 c.-475A>T upstream_gene_variant 1.0 rifampicin
clpC1 4039112 c.1593C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.23 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.23 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.25 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039187 c.1518G>C synonymous_variant 0.28 pyrazinamide
clpC1 4039190 c.1515C>G synonymous_variant 0.25 pyrazinamide
clpC1 4039208 c.1497C>G synonymous_variant 0.23 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4039274 c.1431G>C synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039289 c.1416T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039295 c.1410A>C synonymous_variant 0.24 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039842 c.862_863insT frameshift_variant 1.0 pyrazinamide
panD 4044103 p.Ile60Ser missense_variant 0.91 pyrazinamide
embC 4240789 c.927T>C synonymous_variant 0.2 ethambutol
embA 4245031 p.Arg600Gln missense_variant 1.0 ethambutol
gid 4408218 c.-16G>T upstream_gene_variant 1.0 streptomycin