TB-Profiler result

Run: ERR9786443
Summary

Run ID: ERR9786443

Sample name:

Date: 2024-04-15T21:52:24.523518

Number of reads: 1942629

Percentage reads mapped: 92.82

Median coverage: 89.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 760283 c.477G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760319 c.513C>T synonymous_variant 0.13 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.14 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.14 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762140 c.2334G>C synonymous_variant 0.13 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.14 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.15 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.16 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.14 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.17 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.14 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.16 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.14 rifampicin
rpoC 766327 c.2958C>A synonymous_variant 0.13 rifampicin
rpoC 766345 c.2976T>C synonymous_variant 0.14 rifampicin
rpoC 766357 c.2988C>T synonymous_variant 0.14 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.15 rifampicin
rpoC 766876 c.3507C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766882 c.3513C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.2 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.22 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.21 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.21 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.21 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.2 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.15 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834451 c.910T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834606 c.1065C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.15 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063578 p.Phe384Ser missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289859 c.-618C>T upstream_gene_variant 0.98 pyrazinamide
kasA 2517989 c.-126T>C upstream_gene_variant 0.15 isoniazid
kasA 2517993 c.-122G>T upstream_gene_variant 0.15 isoniazid
ald 3087095 c.276C>T synonymous_variant 1.0 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
lpqB 3625735 c.-825C>T upstream_gene_variant 0.14 bedaquiline
rifampicin
rpoA 3878051 p.Arg153Trp missense_variant 0.95 rifampicin Uncertain significance
rpoA 3878217 c.291A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878232 c.276G>C synonymous_variant 0.15 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.15 rifampicin
rpoA 3878250 c.258C>G synonymous_variant 0.15 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.14 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.16 rifampicin
rpoA 3878310 c.198G>C synonymous_variant 0.15 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.14 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.13 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878938 c.-431T>C upstream_gene_variant 0.14 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
clpC1 4038845 c.1860G>C synonymous_variant 0.16 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.17 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.15 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.15 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.15 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.71 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139496 p.Ala87Gly missense_variant 0.95 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R