TB-Profiler result

Run: ERR4829606
Summary

Run ID: ERR4829606

Sample name:

Date: 2024-10-04T19:13:04.603751

Number of reads: 2599044

Percentage reads mapped: 89.7

Median coverage: 82.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.98
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7490 c.189C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7502 c.201C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7697 c.396C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.98 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.97 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.98 rifampicin Not assoc w R
rpoB 760892 c.1086C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760916 c.1110C>G synonymous_variant 0.14 rifampicin
rpoB 760919 c.1113C>G synonymous_variant 0.14 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.14 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760931 c.1125C>G synonymous_variant 0.13 rifampicin
rpoB 761636 c.1830G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>A synonymous_variant 0.13 rifampicin
rpoB 761648 c.1842T>C synonymous_variant 0.14 rifampicin
rpoC 762410 c.-960T>C upstream_gene_variant 0.13 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762431 c.2625C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762449 c.2643C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 762983 c.-387C>G upstream_gene_variant 0.13 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763050 c.-320C>T upstream_gene_variant 0.14 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763082 c.3276C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763703 c.334_336delTCGinsAGC synonymous_variant 0.15 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.15 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763726 c.357C>T synonymous_variant 0.18 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.16 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.19 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.16 rifampicin
rpoC 763765 c.396T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763771 c.402C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763780 c.411C>G synonymous_variant 0.21 rifampicin
rpoC 763792 p.Glu141Asp missense_variant 0.2 rifampicin
rpoC 763801 c.432C>G synonymous_variant 0.21 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763836 p.Ala156Val missense_variant 0.19 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.16 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.17 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.16 rifampicin
rpoC 763936 c.567C>G synonymous_variant 0.15 rifampicin
rpoC 763939 c.570G>A synonymous_variant 0.15 rifampicin
rpoC 763951 c.582G>A synonymous_variant 0.15 rifampicin
rpoC 763963 c.594C>G synonymous_variant 0.15 rifampicin
rpoC 764167 c.798G>A synonymous_variant 0.13 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>C synonymous_variant 0.14 rifampicin
rpoC 764218 c.849C>T synonymous_variant 0.14 rifampicin
rpoC 764242 c.873C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764245 c.876C>A synonymous_variant 0.15 rifampicin
rpoC 764246 c.877_879delCTCinsTTG synonymous_variant 0.15 rifampicin
rpoC 764263 c.894G>C synonymous_variant 0.17 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.18 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764317 c.948C>G synonymous_variant 0.17 rifampicin
rpoC 764320 c.951C>G synonymous_variant 0.16 rifampicin
rpoC 764389 p.Leu340Phe missense_variant 0.12 rifampicin Uncertain significance
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764428 c.1059G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765622 p.Glu751Asp missense_variant 0.13 rifampicin
rpoC 765883 c.2514C>G synonymous_variant 0.16 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.16 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765934 c.2565C>T synonymous_variant 0.17 rifampicin
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
Rv1258c 1407489 c.-149G>A upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674619 p.Pro140Ser missense_variant 0.14 isoniazid
ethionamide
inhA 1674627 c.426T>C synonymous_variant 0.13 isoniazid
ethionamide
rpsA 1833847 c.306C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.13 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2477c 2783332 c.711T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783347 c.696C>G synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783350 c.693T>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783353 c.690T>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783362 c.681G>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783371 c.672A>G synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783374 c.669G>C synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783410 c.633G>C synonymous_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783419 c.624G>C synonymous_variant 0.19 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783920 c.123G>T synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.14 capreomycin
Rv2752c 3066299 c.-108C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 1.0 rifampicin
bedaquiline
rpoA 3877758 c.750G>C synonymous_variant 0.16 rifampicin
rpoA 3877764 c.744C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877851 c.657C>T synonymous_variant 0.13 rifampicin
rpoA 3877875 c.633T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.13 rifampicin
clpC1 4039022 c.1683A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039025 c.1680C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040000 c.705C>T synonymous_variant 0.15 pyrazinamide
embC 4239298 c.-565C>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
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
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