Run ID: SRR13861456
Sample name:
Date: 2024-10-04T11:43:42.310913
Number of reads: 1288037
Percentage reads mapped: 21.49
Median coverage: 43.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 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 | 375 | p.Asp125Glu | missense_variant | 1.0 | isoniazid | |
gyrB | 4996 | c.-244A>C | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 5258 | p.Lys7* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
gyrB | 7122 | c.1883_1884insA | frameshift_variant | 0.98 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
Rv0010c | 13577 | c.-19G>T | upstream_gene_variant | 1.0 | isoniazid | |
mmaA3 | 738206 | c.-57G>T | upstream_gene_variant | 1.0 | isoniazid | |
mmpL5 | 776374 | p.Arg703Cys | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpR5 | 779126 | p.Cys46Phe | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rplC | 801447 | p.Lys213Asn | missense_variant | 0.98 | linezolid | |
Rv1129c | 1253197 | c.1338C>A | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
Rv1129c | 1253317 | c.1218G>A | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
Rv1129c | 1253639 | p.Leu299* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
fbiC | 1303004 | p.Ala25Glu | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1303171 | p.Arg81Trp | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1303517 | p.Met196Thr | missense_variant | 0.97 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv1258c | 1407597 | c.-257C>G | upstream_gene_variant | 1.0 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.23 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.25 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.25 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.18 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.54 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.57 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rpsA | 1834640 | p.Glu367* | stop_gained | 0.93 | pyrazinamide | Uncertain significance |
bacA | 2064395 | p.Thr112Pro | missense_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
bacA | 2064589 | c.139delT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
ndh | 2103004 | c.39T>G | synonymous_variant | 1.0 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
PPE35 | 2170453 | p.Gly54Ser | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2223326 | c.-162C>T | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223365 | c.-201C>A | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
pncA | 2288748 | p.Ala165Asp | missense_variant | 1.0 | pyrazinamide | |
kasA | 2518474 | p.Glu120Asp | missense_variant | 1.0 | isoniazid | |
thyX | 3067529 | c.417C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073764 | c.708T>C | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073862 | p.Gly204Ser | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073963 | p.Leu170Gln | missense_variant | 0.98 | para-aminosalicylic_acid | |
fbiD | 3339357 | c.240G>T | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv3083 | 3448352 | c.-152G>C | upstream_gene_variant | 1.0 | ethionamide | |
Rv3083 | 3449624 | p.Lys374Met | missense_variant | 1.0 | ethionamide | |
Rv3083 | 3449919 | c.1416C>A | synonymous_variant | 1.0 | ethionamide | |
fbiB | 3642227 | p.Gln231His | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiB | 3642581 | c.1047A>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
embA | 4244641 | p.Val470Gly | missense_variant | 1.0 | ethambutol | |
embA | 4245197 | c.1965C>T | synonymous_variant | 0.93 | ethambutol | Not assoc w R - Interim |
embB | 4246641 | p.Ala43Glu | missense_variant | 1.0 | ethambutol | |
embB | 4247233 | p.Asp240Glu | missense_variant | 1.0 | ethambutol | |
ethA | 4327035 | p.Tyr147Asp | missense_variant | 1.0 | ethionamide | |
ethR | 4327923 | p.Gln125His | missense_variant | 1.0 | ethionamide |