Run ID: SAMN02381051
Sample name:
Date: 2024-04-15T14:31:19.506028
Number of reads: 4326379
Percentage reads mapped: 39.09
Median coverage: 81.0
Strain: lineage4.6.1.2
Spoligotype:
Drug-resistance: RR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 0.99 |
lineage4.6.1.2 | Euro-American | RD724 | 0.99 |
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 | ||||
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 |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.96 | rifampicin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6501 | p.Arg421His | missense_variant | 0.97 | levofloxacin | |
moxifloxacin | ||||||
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 | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
nusG | 734624 | p.Arg124Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 762887 | c.3081G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 762899 | c.3093G>C | synonymous_variant | 0.22 | rifampicin | Not assoc w R - Interim |
rpoB | 762917 | c.3111C>G | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoB | 762920 | c.3114C>T | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoB | 762923 | c.3117C>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.19 | rifampicin | |
rpoB | 762934 | c.3129_3130insAGCC | frameshift_variant | 0.19 | rifampicin | |
rpoB | 762938 | c.3133_3136delATGA | frameshift_variant | 0.19 | rifampicin | |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.18 | rifampicin | |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.2 | rifampicin | |
rpoC | 764587 | c.1218C>G | synonymous_variant | 0.24 | rifampicin | |
rpoC | 764593 | c.1224C>T | synonymous_variant | 0.28 | rifampicin | |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.36 | rifampicin | Not assoc w R - Interim |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.37 | rifampicin | Not assoc w R - Interim |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.37 | rifampicin | Not assoc w R - Interim |
rpoC | 764641 | c.1272C>T | synonymous_variant | 0.39 | rifampicin | Not assoc w R - Interim |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.39 | rifampicin | Not assoc w R - Interim |
rpoC | 764663 | p.Val432Thr | missense_variant | 0.33 | rifampicin | |
rpoC | 764672 | p.Gln435Glu | missense_variant | 0.32 | rifampicin | |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.3 | rifampicin | Not assoc w R - Interim |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.2 | rifampicin | |
rpoC | 764701 | c.1332C>G | synonymous_variant | 0.11 | 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 | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253900 | p.Leu212Arg | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1416410 | p.Leu313Arg | missense_variant | 0.99 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.54 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Uncertain significance | |||||
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.49 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.41 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.38 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472264 | n.419T>C | non_coding_transcript_exon_variant | 0.35 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472266 | n.421C>A | non_coding_transcript_exon_variant | 0.35 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.26 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472338 | n.493A>C | non_coding_transcript_exon_variant | 0.22 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.25 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.27 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472382 | n.537G>T | non_coding_transcript_exon_variant | 0.26 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.25 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.22 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472415 | n.570T>A | non_coding_transcript_exon_variant | 0.22 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472422 | n.577T>C | non_coding_transcript_exon_variant | 0.19 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Uncertain significance | |||||
rrs | 1472714 | n.869A>T | non_coding_transcript_exon_variant | 0.25 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472715 | n.870C>A | non_coding_transcript_exon_variant | 0.24 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.25 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472770 | n.925C>T | non_coding_transcript_exon_variant | 0.42 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.39 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.33 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472812 | n.967A>C | non_coding_transcript_exon_variant | 0.28 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472826 | n.981G>C | non_coding_transcript_exon_variant | 0.16 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474182 | n.525C>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1474184 | n.527C>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1474185 | n.528G>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1474199 | n.542G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
linezolid | ||||||
rrl | 1474201 | n.544T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474228 | n.571T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474235 | n.578delGinsAT | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1474249 | n.592G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.78 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.66 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476491 | n.2834T>C | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
linezolid | ||||||
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
inhA | 1674465 | c.264C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
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 | 2154874 | p.Tyr413Cys | missense_variant | 0.99 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2681 | 2996876 | c.138A>C | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 0.97 | streptomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Not assoc w R | |||||
glpK | 4139670 | p.Cys29Tyr | missense_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Uncertain significance | |||||
isoniazid | 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 |
ethR | 4328183 | p.Tyr212Cys | missense_variant | 0.98 | ethionamide | |
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 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |