Run ID: ERR9634265
Sample name:
Date: 2024-10-04T02:47:17.844096
Number of reads: 220869
Percentage reads mapped: 68.97
Median coverage: 5.0
Strain: lineage4.3.4.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.5 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.31 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 0.87 |
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 |
---|---|---|---|---|---|---|
gyrA | 7523 | c.222C>G | synonymous_variant | 0.5 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7526 | c.225G>C | synonymous_variant | 0.5 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7532 | c.231T>C | synonymous_variant | 0.53 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7541 | c.240C>G | synonymous_variant | 0.5 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7547 | c.246C>T | synonymous_variant | 0.5 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7559 | c.258G>C | synonymous_variant | 0.47 | levofloxacin | Not assoc w R - Interim |
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 | 7622 | c.321C>T | synonymous_variant | 0.67 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7631 | c.330G>C | synonymous_variant | 0.71 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7637 | c.336C>T | synonymous_variant | 0.68 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7652 | c.351C>T | synonymous_variant | 0.67 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7658 | c.357A>G | synonymous_variant | 0.59 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7661 | c.360C>T | synonymous_variant | 0.59 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7664 | c.363T>C | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7667 | c.366C>T | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7670 | c.369A>G | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7676 | c.375G>C | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7679 | c.378G>C | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7683 | c.382_384delAGGinsCGT | synonymous_variant | 0.62 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7694 | c.393A>G | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7697 | c.396C>G | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7706 | c.405C>T | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7709 | c.408G>C | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7710 | c.409T>C | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7728 | c.427_429delAGGinsCGT | synonymous_variant | 0.65 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7760 | c.459C>T | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7763 | c.462T>G | synonymous_variant | 0.61 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7784 | c.483A>G | synonymous_variant | 0.46 | levofloxacin | |
moxifloxacin | ||||||
ccsA | 620604 | c.714C>G | synonymous_variant | 0.58 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620605 | p.Val239Ile | missense_variant | 0.58 | kanamycin | Uncertain significance |
capreomycin | ||||||
amikacin | Uncertain significance | |||||
ccsA | 620619 | c.729G>C | synonymous_variant | 0.58 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620622 | c.732G>C | synonymous_variant | 0.58 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620625 | c.735A>C | synonymous_variant | 0.58 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620649 | c.759A>G | synonymous_variant | 0.71 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620658 | c.768C>T | synonymous_variant | 0.67 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620676 | c.786C>T | synonymous_variant | 0.7 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620694 | c.804C>G | synonymous_variant | 0.75 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620698 | p.Val270Ile | missense_variant | 0.75 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620730 | c.840C>T | synonymous_variant | 0.62 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620733 | c.843G>C | synonymous_variant | 0.64 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620736 | c.846G>C | synonymous_variant | 0.62 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620739 | c.849A>G | synonymous_variant | 0.62 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620742 | c.852G>C | synonymous_variant | 0.62 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620748 | c.858T>C | synonymous_variant | 0.65 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620766 | c.876C>A | synonymous_variant | 0.65 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620778 | c.888T>C | synonymous_variant | 0.64 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620783 | p.Ala298Val | missense_variant | 0.67 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620793 | c.903G>C | synonymous_variant | 0.59 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620796 | c.906C>G | synonymous_variant | 0.6 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620802 | c.912C>G | synonymous_variant | 0.57 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620808 | c.918T>C | synonymous_variant | 0.54 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ccsA | 620809 | c.919C>T | synonymous_variant | 0.54 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
ccsA | 620818 | p.Val310Ile | missense_variant | 0.55 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
nusG | 734421 | c.168A>C | synonymous_variant | 0.62 | rifampicin | |
nusG | 734424 | c.171G>C | synonymous_variant | 0.64 | rifampicin | |
nusG | 734439 | c.186C>G | synonymous_variant | 0.71 | rifampicin | |
nusG | 734442 | c.189G>A | synonymous_variant | 0.71 | rifampicin | |
nusG | 734451 | c.198G>C | synonymous_variant | 0.75 | rifampicin | |
nusG | 734454 | c.201A>G | synonymous_variant | 0.75 | rifampicin | |
nusG | 734460 | c.207G>C | synonymous_variant | 0.75 | rifampicin | |
nusG | 734472 | c.219T>G | synonymous_variant | 0.8 | rifampicin | Not assoc w R - Interim |
nusG | 734475 | c.222T>C | synonymous_variant | 0.8 | rifampicin | Not assoc w R - Interim |
nusG | 734499 | c.246G>C | synonymous_variant | 0.86 | rifampicin | |
nusG | 734532 | c.279A>G | synonymous_variant | 0.91 | rifampicin | Not assoc w R - Interim |
rpoB | 760181 | c.375T>C | synonymous_variant | 0.7 | rifampicin | Not assoc w R - Interim |
rpoB | 760184 | c.378A>G | synonymous_variant | 0.73 | rifampicin | Not assoc w R - Interim |
rpoB | 760196 | c.390C>G | synonymous_variant | 0.7 | rifampicin | Not assoc w R - Interim |
rpoC | 765496 | c.2127C>G | synonymous_variant | 0.5 | rifampicin | |
rpoC | 765499 | c.2130C>G | synonymous_variant | 0.5 | rifampicin | Not assoc w R - Interim |
rpoC | 765533 | p.Tyr722His | missense_variant | 0.46 | rifampicin | Uncertain significance |
mmpL5 | 775856 | c.2625T>C | synonymous_variant | 0.71 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775862 | c.2619G>C | synonymous_variant | 0.62 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775865 | c.2616T>C | synonymous_variant | 0.62 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775886 | c.2595A>C | synonymous_variant | 0.67 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775904 | c.2577G>A | synonymous_variant | 0.78 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775910 | c.2571G>A | synonymous_variant | 0.82 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775916 | c.2565T>C | synonymous_variant | 0.73 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775922 | c.2559G>C | synonymous_variant | 0.5 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775951 | c.2530C>T | synonymous_variant | 0.67 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775961 | c.2520C>G | synonymous_variant | 0.86 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775966 | p.Ala839Ser | missense_variant | 0.65 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775970 | c.2511G>C | synonymous_variant | 0.7 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775975 | c.2506T>C | synonymous_variant | 0.82 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775981 | p.Leu834Met | missense_variant | 0.82 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775991 | c.2490G>A | synonymous_variant | 0.79 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775994 | p.Ile829Leu | missense_variant | 0.71 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776000 | p.Leu827Ile | missense_variant | 0.77 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776005 | p.Ile826Leu | missense_variant | 0.77 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776009 | c.2472A>G | synonymous_variant | 0.77 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776030 | c.2451G>T | synonymous_variant | 0.77 | bedaquiline | |
clofazimine | ||||||
rpsL | 781682 | c.123T>C | synonymous_variant | 0.64 | streptomycin | |
rpsL | 781709 | c.150G>C | synonymous_variant | 0.77 | streptomycin | Not assoc w R - Interim |
rpsL | 781715 | c.156T>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781718 | c.159C>G | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781728 | c.169T>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781733 | c.174G>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781736 | c.177T>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781737 | p.Gln60Gly | missense_variant | 0.77 | streptomycin | |
rpsL | 781742 | c.183C>T | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781751 | c.192G>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781754 | c.195G>C | synonymous_variant | 0.77 | streptomycin | |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.71 | streptomycin | |
rpsL | 781766 | c.207C>T | synonymous_variant | 0.71 | streptomycin | Not assoc w R - Interim |
fbiC | 1304613 | c.1683T>C | synonymous_variant | 0.61 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304634 | c.1704C>G | synonymous_variant | 0.65 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304640 | c.1710A>C | synonymous_variant | 0.62 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304646 | c.1716T>C | synonymous_variant | 0.62 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304652 | c.1722C>G | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304658 | c.1728C>G | synonymous_variant | 0.59 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304661 | c.1731C>T | synonymous_variant | 0.56 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304670 | c.1740G>C | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304671 | p.Val581Thr | missense_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304675 | p.Gly582Asp | missense_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304694 | c.1764A>C | synonymous_variant | 0.62 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304703 | c.1773C>G | synonymous_variant | 0.54 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304715 | c.1785G>T | synonymous_variant | 0.54 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304724 | c.1794A>G | synonymous_variant | 0.58 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fbiC | 1304727 | c.1797A>C | synonymous_variant | 0.57 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304736 | c.1806G>A | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304739 | c.1809C>A | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304748 | c.1818T>C | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304751 | c.1821C>G | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304757 | c.1827A>G | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304760 | c.1830G>C | synonymous_variant | 0.53 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
sigE | 1364919 | c.507T>C | synonymous_variant | 0.73 | pyrazinamide | |
sigE | 1364922 | p.Glu170Asp | missense_variant | 0.7 | pyrazinamide | |
sigE | 1364950 | p.Ala180Ser | missense_variant | 0.82 | pyrazinamide | |
sigE | 1364955 | c.543G>A | synonymous_variant | 0.82 | pyrazinamide | |
sigE | 1364962 | p.Pro184Ala | missense_variant | 0.73 | pyrazinamide | |
sigE | 1364967 | c.555C>T | synonymous_variant | 0.67 | pyrazinamide | |
sigE | 1364976 | c.564T>C | synonymous_variant | 0.73 | pyrazinamide | Not assoc w R - Interim |
sigE | 1364980 | c.568_570delTTGinsCTC | synonymous_variant | 0.73 | pyrazinamide | |
sigE | 1364984 | p.Ala191Asp | missense_variant | 0.73 | pyrazinamide | |
sigE | 1364992 | p.Pro194Ala | missense_variant | 0.73 | pyrazinamide | |
sigE | 1365003 | c.591T>C | synonymous_variant | 0.73 | pyrazinamide | |
sigE | 1365006 | c.594T>C | synonymous_variant | 0.73 | pyrazinamide | |
sigE | 1365015 | c.603G>C | synonymous_variant | 0.67 | pyrazinamide | |
sigE | 1365018 | c.606G>C | synonymous_variant | 0.67 | pyrazinamide | |
sigE | 1365042 | c.630G>C | synonymous_variant | 0.67 | pyrazinamide | |
rrs | 1472847 | n.1002G>C | non_coding_transcript_exon_variant | 0.88 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472848 | n.1003T>A | non_coding_transcript_exon_variant | 0.88 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472849 | n.1004C>G | non_coding_transcript_exon_variant | 0.88 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472858 | n.1013G>T | non_coding_transcript_exon_variant | 0.88 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472859 | n.1014G>T | non_coding_transcript_exon_variant | 0.88 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472860 | n.1015C>G | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.72 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rpsA | 1833745 | c.204G>C | synonymous_variant | 0.75 | pyrazinamide | |
rpsA | 1833772 | c.231C>T | synonymous_variant | 0.88 | pyrazinamide | |
rpsA | 1833787 | c.246C>G | synonymous_variant | 0.94 | pyrazinamide | |
rpsA | 1833790 | c.249T>C | synonymous_variant | 0.94 | pyrazinamide | |
rpsA | 1833793 | c.252C>T | synonymous_variant | 0.95 | pyrazinamide | |
rpsA | 1833802 | c.261A>G | synonymous_variant | 0.95 | pyrazinamide | |
rpsA | 1833808 | c.267G>C | synonymous_variant | 0.95 | pyrazinamide | |
rpsA | 1833811 | c.270G>T | synonymous_variant | 0.95 | pyrazinamide | |
rpsA | 1833820 | c.279G>A | synonymous_variant | 0.9 | pyrazinamide | |
rpsA | 1833832 | c.291G>A | synonymous_variant | 0.87 | pyrazinamide | |
rpsA | 1833838 | c.297G>A | synonymous_variant | 0.87 | pyrazinamide | |
rpsA | 1833841 | c.300C>G | synonymous_variant | 0.82 | pyrazinamide | |
rpsA | 1833847 | c.306C>G | synonymous_variant | 0.77 | pyrazinamide | |
rpsA | 1833856 | c.315A>G | synonymous_variant | 0.75 | pyrazinamide | |
rpsA | 1833862 | c.321G>T | synonymous_variant | 0.79 | pyrazinamide | |
rpsA | 1833892 | c.351G>A | synonymous_variant | 0.72 | pyrazinamide | |
rpsA | 1833894 | p.Ala118Glu | missense_variant | 0.72 | pyrazinamide | |
rpsA | 1833904 | c.363G>A | synonymous_variant | 0.65 | pyrazinamide |