Run ID: ERR11466014
Sample name:
Date: 2024-04-14T23:03:33.996047
Number of reads: 3682839
Percentage reads mapped: 99.76
Median coverage: 93.0
Strain: lineage4.3.4.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4.2.1 | Euro-American (LAM) | RD174 | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 1.0 |
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 10 | p.Asp4His | missense_variant | 1.0 | isoniazid | Uncertain significance |
gyrB | 6140 | p.Val301Leu | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 761027 | c.1221A>G | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
rpoB | 762233 | c.2427G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 762236 | c.2430G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 762254 | c.2448T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 762257 | c.2451C>G | synonymous_variant | 0.15 | rifampicin | |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.18 | rifampicin | |
rpoB | 762275 | c.2469C>G | synonymous_variant | 0.19 | rifampicin | |
rpoB | 762284 | c.2478G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 763528 | c.159G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763534 | c.165T>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 763537 | c.168C>G | synonymous_variant | 0.17 | rifampicin | |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763573 | c.204G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763636 | c.267T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 763741 | c.372C>T | synonymous_variant | 0.13 | rifampicin | |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764536 | c.1167G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 764578 | c.1209C>G | synonymous_variant | 0.12 | rifampicin | |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.12 | rifampicin | |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.12 | rifampicin | |
rpoC | 764587 | c.1218C>G | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766393 | c.3024C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.11 | clofazimine | |
bedaquiline | ||||||
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 | 1472148 | n.303T>C | non_coding_transcript_exon_variant | 0.11 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472234 | n.389T>C | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472974 | n.1129A>G | non_coding_transcript_exon_variant | 0.21 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.35 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.32 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472996 | n.1151T>C | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.12 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473062 | n.1217T>G | non_coding_transcript_exon_variant | 0.11 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474558 | n.901G>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474676 | n.1019T>A | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474905 | n.1248T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474913 | n.1256T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475028 | n.1371G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476164 | n.2507A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1833769 | c.228C>G | synonymous_variant | 0.12 | 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 |
katG | 2155410 | c.702G>C | synonymous_variant | 0.1 | isoniazid | Not assoc w R - Interim |
PPE35 | 2169902 | c.709_711delCTGinsTC | frameshift_variant&synonymous_variant | 0.18 | pyrazinamide | Uncertain significance |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.22 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840719 | c.702A>G | synonymous_variant | 1.0 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4039610 | c.1095G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039787 | c.918G>C | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039790 | c.915C>G | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039904 | c.801A>G | synonymous_variant | 0.12 | pyrazinamide | |
glpK | 4138643 | c.1113A>G | synonymous_variant | 0.13 | ethambutol | Not assoc w R - Interim |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
glpK | 4138646 | c.1110G>C | synonymous_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
glpK | 4138734 | p.Ser341Thr | missense_variant | 0.11 | 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 | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |