Run ID: ERR2600561
Sample name:
Date: 2024-03-24T15:43:41.911979
Number of reads: 848208
Percentage reads mapped: 81.47
Median coverage: 18.0
Strain: lineage2.2.1;lineage4.8
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.28 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.27 |
lineage4 | Euro-American | None | 0.74 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.65 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | embB | p.Gly406Ala | Assoc w R | |
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
capreomycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
kanamycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
cycloserine | ||||
ethionamide | ethA | c.341delA | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance | Mutation from literature |
kanamycin | Uncertain significance | Mutation from literature | |||||
amikacin | Uncertain significance | Mutation from literature | |||||
embB | 4247730 | p.Gly406Ala | missense_variant | 0.33 | ethambutol | Assoc w R | |
ethA | 4327132 | c.341delA | frameshift_variant | 0.35 | 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 | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.33 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.5 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.48 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.31 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.31 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.29 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.29 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.33 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.4 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473270 | n.1425G>A | non_coding_transcript_exon_variant | 0.31 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1474558 | n.901G>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474584 | n.927C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | ||||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474831 | n.1174A>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | ||||||
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.39 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.39 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.51 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.38 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476515 | n.2858C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
linezolid | ||||||
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476539 | n.2882A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.69 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.71 | para-aminosalicylic_acid | |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.37 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.53 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.4 | ethambutol | Not assoc w R |
embA | 4244510 | c.1278G>A | synonymous_variant | 0.6 | ethambutol | Not assoc w R - Interim |
embB | 4247309 | p.Arg266Ser | missense_variant | 0.32 | ethambutol | |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.41 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.42 | streptomycin | Not assoc w R |