TB-Profiler result

Run: ERR12268496
Summary

Run ID: ERR12268496

Sample name:

Date: 2024-10-04T21:14:08.707234

Number of reads: 1473957

Percentage reads mapped: 95.5

Median coverage: 39.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 Euro-American None 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 760181 c.375T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761885 c.2079T>C synonymous_variant 0.16 rifampicin
rpoB 761948 c.2142G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.2 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.2 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.19 rifampicin
rpoC 764131 c.762T>C synonymous_variant 0.19 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764236 c.867G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764248 c.879C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.28 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.28 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.15 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.22 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.16 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
rpoC 766795 c.3426C>T synonymous_variant 0.15 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.15 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.26 rifampicin
rpoC 766963 c.3594T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.17 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.18 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.18 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.28 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.23 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.19 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800648 c.-161A>T upstream_gene_variant 0.22 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.2 linezolid
rplC 800693 c.-116A>G upstream_gene_variant 0.26 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.22 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.23 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.23 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.24 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.22 linezolid
fbiC 1303836 c.906G>C synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1303845 c.915C>G synonymous_variant 0.2 pretomanid
delamanid
clofazimine
fbiC 1303846 p.Phe306Val missense_variant 0.2 pretomanid
delamanid
clofazimine
Rv1258c 1406239 p.Gly368Ser missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.32 capreomycin
linezolid Uncertain significance
rpsA 1833838 c.297G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.16 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 1.0 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3627254 c.-641C>T upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrB 3627263 c.-650C>T upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrB 3627266 c.-653A>G upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3627272 c.-659G>T upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrB 3627275 c.-662G>T upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3627296 c.-683T>C upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3627299 c.-688_-686delTTGinsCTA upstream_gene_variant 0.26 rifampicin
bedaquiline
mtrB 3627314 c.-701C>T upstream_gene_variant 0.25 rifampicin
bedaquiline
mtrB 3627317 c.-704T>C upstream_gene_variant 0.25 rifampicin
bedaquiline
rpoA 3877587 c.921A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.18 rifampicin
clpC1 4040522 c.183T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248157 c.1644A>G synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embB 4248172 c.1659G>C synonymous_variant 0.24 ethambutol
embB 4248199 c.1686A>G synonymous_variant 0.16 ethambutol
embB 4248200 p.Ile563Val missense_variant 0.16 ethambutol
embB 4248205 c.1692C>G synonymous_variant 0.17 ethambutol
embB 4248206 p.Ser565Gly missense_variant 0.18 ethambutol Uncertain significance
embB 4248220 c.1707A>C synonymous_variant 0.2 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin