Run ID: SRR1173832
Sample name:
Date: 2025-02-11T19:23:37.939782
Number of reads: 738172
Percentage reads mapped: 39.63
Median coverage: 15.0
Strain: lineage3.1;lineage4.6.1.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.62 |
lineage4.6 | Euro-American | None | 0.25 |
lineage4.6.1.1 | Euro-American | RD724 | 0.21 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.21 |
lineage3.1 | East-African-Indian | RD750 | 0.6 |
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 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.68 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.62 | ethionamide | Not assoc w R - Interim |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.79 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.75 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.71 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.38 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.31 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.49 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.32 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.59 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.41 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.71 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.62 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
linezolid | ||||||
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475575 | n.1918C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1475576 | n.1919C>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.72 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.72 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.51 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
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 | 2154724 | p.Arg463Leu | missense_variant | 0.45 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.76 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.82 | isoniazid | Not assoc w R |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.74 | cycloserine | |
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 0.73 | kanamycin | Not assoc w R |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.81 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.88 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4241562 | p.Arg567His | missense_variant | 0.56 | ethambutol | Not assoc w R |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.67 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407742 | p.Arg154Gln | missense_variant | 0.39 | streptomycin |