Run ID: ERR3078008
Sample name:
Date: 2024-10-04T20:22:09.280293
Number of reads: 872269
Percentage reads mapped: 4.86
Median coverage: 20.0
Strain: lineage4.6.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 0.97 |
lineage4 | Euro-American | None | 0.97 |
lineage4.6.1.1 | Euro-American | RD724 | 0.27 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.93 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Gly442Glu | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
p.Leu443Ile | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
p.Leu449Val | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | ahpC | c.-54C>T | Uncertain significance | Mutation from literature |
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 | 761131 | p.Gly442Glu | missense_variant | 0.23 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoB | 761133 | p.Leu443Ile | missense_variant | 0.23 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoB | 761151 | p.Leu449Val | missense_variant | 0.21 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
ahpC | 2726139 | c.-54C>T | upstream_gene_variant | 0.82 | isoniazid | 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 | 7539 | p.Thr80Ala | missense_variant | 0.86 | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575110 | c.-238C>T | upstream_gene_variant | 0.94 | isoniazid | |
ethionamide | ||||||
rpoB | 761126 | c.1320G>T | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.21 | rifampicin | |
rpoB | 761159 | c.1353G>A | synonymous_variant | 0.22 | rifampicin | |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.21 | rifampicin | |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.21 | rifampicin | |
rpoB | 761178 | p.Ser458Thr | missense_variant | 0.21 | rifampicin | Uncertain significance |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.28 | rifampicin | Not assoc w R - Interim |
rpoB | 761196 | p.Leu464Phe | missense_variant | 0.24 | rifampicin | |
rpoB | 761204 | c.1398C>G | synonymous_variant | 0.25 | rifampicin | |
rpoB | 761207 | c.1401C>T | synonymous_variant | 0.29 | rifampicin | |
rpoB | 761220 | p.Ser472Thr | missense_variant | 0.25 | rifampicin | |
rpoB | 761234 | c.1428G>T | synonymous_variant | 0.25 | rifampicin | |
rpoB | 761235 | p.Met477Val | missense_variant | 0.25 | rifampicin | |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.53 | rifampicin | |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.51 | rifampicin | Uncertain significance |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.51 | rifampicin | |
rpoB | 762899 | c.3093G>C | synonymous_variant | 0.53 | rifampicin | Not assoc w R - Interim |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.53 | rifampicin | |
rpoB | 762917 | c.3111C>G | synonymous_variant | 0.53 | rifampicin | Not assoc w R - Interim |
rpoB | 762920 | c.3114C>T | synonymous_variant | 0.53 | rifampicin | Not assoc w R - Interim |
rpoB | 762929 | c.3123G>T | synonymous_variant | 0.5 | rifampicin | Not assoc w R - Interim |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.5 | rifampicin | |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.49 | rifampicin | |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.49 | rifampicin | |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.5 | rifampicin | Uncertain significance |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.56 | rifampicin | |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.54 | rifampicin | |
rpoB | 762989 | c.3183G>T | synonymous_variant | 0.55 | rifampicin | Not assoc w R - Interim |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.42 | rifampicin | |
rpoB | 763014 | p.Met1070Leu | missense_variant | 0.29 | rifampicin | |
rpoB | 763017 | p.Gln1071Glu | missense_variant | 0.25 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472374 | n.529T>A | non_coding_transcript_exon_variant | 0.43 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.41 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.36 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.37 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.39 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472694 | n.849C>G | non_coding_transcript_exon_variant | 0.38 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.45 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.61 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.62 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.62 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.74 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.77 | 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 | 0.73 | 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 | 0.7 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.55 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472839 | n.994C>G | non_coding_transcript_exon_variant | 0.48 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.95 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.95 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.95 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.95 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.95 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.95 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.94 | 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 | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.93 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.93 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.9 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.84 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.81 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.81 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.79 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1475518 | n.1861A>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.74 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | ||||||
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 | 2102116 | c.927G>T | synonymous_variant | 0.96 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726507 | c.315G>T | synonymous_variant | 0.85 | isoniazid | |
Rv2681 | 2996876 | c.138A>C | synonymous_variant | 0.92 | capreomycin | Not assoc w R |
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
glpK | 4139670 | p.Cys29Tyr | missense_variant | 0.94 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4328329 | c.-856C>G | upstream_gene_variant | 1.0 | ethionamide | |
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 |