Run ID: SRR6397579
Sample name:
Date: 2024-10-05T02:28:56.590095
Number of reads: 5679076
Percentage reads mapped: 95.22
Median coverage: 159.0
Strain: lineage4.4.1.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1.2 | Euro-American | None | 0.99 |
lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
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 | ||||
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 | 0.13 | amikacin | Uncertain significance | Mutation from literature |
capreomycin | Uncertain significance | Mutation from literature | |||||
kanamycin | Uncertain significance | Mutation from literature |
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 | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 779565 | c.-660G>C | upstream_gene_variant | 0.99 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471658 | n.-188T>C | upstream_gene_variant | 0.99 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472582 | n.737G>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472585 | n.740A>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472623 | n.778A>C | non_coding_transcript_exon_variant | 0.25 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472647 | n.802C>T | non_coding_transcript_exon_variant | 0.22 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472673 | n.828T>G | non_coding_transcript_exon_variant | 0.19 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472675 | n.830T>C | non_coding_transcript_exon_variant | 0.2 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472677 | n.832C>A | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472682 | n.837T>A | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472683 | n.838T>C | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472687 | n.842A>T | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472707 | n.862A>T | non_coding_transcript_exon_variant | 0.19 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472767 | n.922G>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472954 | n.1110delC | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472958 | n.1113_1114insC | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472986 | n.1141_1142insA | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472989 | n.1145delA | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472996 | n.1151T>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474506 | n.849C>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474507 | n.850G>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474516 | n.859C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1474529 | n.872A>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474530 | n.873G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474539 | n.882C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474540 | n.883T>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474552 | n.895C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474558 | n.901G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474779 | n.1122G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474780 | n.1123C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474782 | n.1125G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474799 | n.1143delT | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1474803 | n.1146_1147insA | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1474806 | n.1149A>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474830 | n.1173A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474831 | n.1174A>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1475877 | n.2220C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475892 | n.2235A>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.1 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476204 | n.2547C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476235 | n.2578A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476363 | n.2706A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476366 | n.2709A>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476374 | n.2717T>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
katG | 2153960 | p.Pro718Ser | missense_variant | 1.0 | isoniazid | Uncertain significance |
PPE35 | 2167770 | p.Ser948Ile | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | 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 | |||||
pepQ | 2860213 | p.Pro69Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.99 | ethionamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4040945 | c.-241G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.98 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249012 | c.2499G>A | synonymous_variant | 0.99 | 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 |