Run ID: ERR2124081
Sample name:
Date: 2024-10-04T12:41:18.021489
Number of reads: 6279755
Percentage reads mapped: 99.38
Median coverage: 68.0
Strain: lineage4.6.1.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 1.0 |
lineage4.6.1.2 | Euro-American | RD724 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.99 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.His43Pro | Assoc w R - Interim | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1215_1224delGTTGAATTAC | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289114 | p.His43Pro | missense_variant | 0.98 | pyrazinamide | Assoc w R - Interim | |
embB | 4247429 | p.Met306Val | missense_variant | 0.96 | ethambutol | Assoc w R | |
ethA | 4326249 | c.1215_1224delGTTGAATTAC | frameshift_variant | 1.0 | ethionamide | Assoc w R |
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 | 7539 | p.Thr80Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R - Interim | |||||
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 | |||||
rpoC | 764660 | p.Val431Met | missense_variant | 0.98 | rifampicin | Uncertain significance |
rpoC | 764810 | p.Pro481Thr | missense_variant | 0.99 | rifampicin | Uncertain significance |
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 |
embR | 1416410 | p.Leu313Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
linezolid | ||||||
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473944 | n.287G>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
linezolid | ||||||
rrl | 1473981 | n.324delGinsAT | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
linezolid | ||||||
rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
linezolid | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1474716 | n.1059A>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
linezolid | ||||||
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1475289 | n.1632G>A | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475297 | n.1640C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.96 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2170692 | c.-80T>G | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2714308 | p.Pro342Leu | missense_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
Rv2681 | 2996876 | c.138A>C | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 0.98 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
glpK | 4139670 | p.Cys29Tyr | missense_variant | 0.98 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245055 | p.Thr608Asn | missense_variant | 1.0 | ethambutol | Uncertain significance |
ubiA | 4269124 | p.Ala237Val | missense_variant | 0.99 | ethambutol | Uncertain significance |
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 | 0.99 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408094 | p.Gly37Arg | missense_variant | 0.97 | streptomycin | Uncertain significance |