Run ID: ERR11465151
Sample name:
Date: 2024-10-04T02:54:24.686866
Number of reads: 1435501
Percentage reads mapped: 99.11
Median coverage: 30.0
Strain: lineage4.3.4.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
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 |
---|---|---|---|---|---|---|
dnaA | 546 | c.546C>G | synonymous_variant | 0.12 | isoniazid | |
gyrA | 6634 | c.-668T>C | upstream_gene_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 6640 | c.-662A>C | upstream_gene_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 6643 | c.-659A>G | upstream_gene_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 6655 | c.-647T>C | upstream_gene_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6745 | c.1506T>C | synonymous_variant | 0.15 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrB | 6775 | c.1536G>C | synonymous_variant | 0.16 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 6781 | c.-521C>T | upstream_gene_variant | 0.16 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6793 | c.1554T>C | synonymous_variant | 0.12 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrB | 6798 | p.Gly520Ala | missense_variant | 0.16 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
gyrB | 6824 | c.1585C>T | synonymous_variant | 0.17 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
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 | 8250 | p.Glu317Gln | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13483 | p.Ala26Thr | missense_variant | 1.0 | isoniazid | Uncertain significance |
hadA | 731789 | c.-141A>G | upstream_gene_variant | 0.19 | isoniazid | |
nusG | 734499 | c.246G>C | synonymous_variant | 0.21 | rifampicin | |
nusG | 734910 | c.657C>G | synonymous_variant | 0.17 | rifampicin | |
rpoB | 760118 | c.312T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 760121 | c.315T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 760184 | c.378A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 760196 | c.390C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 761954 | c.2148C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 761999 | c.2193G>C | synonymous_variant | 0.12 | rifampicin | |
rpoB | 762008 | c.2202C>T | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 762038 | c.2232C>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 763127 | c.3321G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 763142 | c.-228C>G | upstream_gene_variant | 0.13 | rifampicin | |
rpoC | 763259 | c.-111G>C | upstream_gene_variant | 0.12 | rifampicin | |
rpoB | 763268 | c.3462C>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 763660 | c.291T>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763675 | c.306C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.13 | rifampicin | |
rpoC | 763741 | c.372C>T | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764239 | c.870T>C | synonymous_variant | 0.32 | rifampicin | |
rpoC | 764245 | c.876C>T | synonymous_variant | 0.3 | rifampicin | |
rpoC | 764431 | c.1062G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764746 | c.1377G>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 764791 | c.1422C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764797 | c.1428G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.93 | rifampicin | Not assoc w R |
rpoC | 765826 | c.2457T>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 766504 | c.3135G>C | synonymous_variant | 0.23 | rifampicin | |
rpoC | 766517 | p.Thr1050Ala | missense_variant | 0.25 | rifampicin | |
rpoC | 766522 | c.3153C>A | synonymous_variant | 0.25 | rifampicin | |
rpoC | 766525 | c.3156G>C | synonymous_variant | 0.23 | rifampicin | |
rpoC | 766528 | c.3159T>G | synonymous_variant | 0.23 | rifampicin | |
rpoC | 766530 | p.Arg1054Gln | missense_variant | 0.22 | rifampicin | |
rpoC | 766537 | c.3168G>A | synonymous_variant | 0.22 | rifampicin | |
rpoC | 766540 | p.Asp1057Glu | missense_variant | 0.22 | rifampicin | |
rpoC | 766546 | p.Glu1059Asp | missense_variant | 0.22 | rifampicin | |
rpoC | 766549 | c.3180G>C | synonymous_variant | 0.21 | rifampicin | |
rpoC | 766843 | c.3474T>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 766846 | c.3477C>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
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 |
rplC | 800633 | c.-176T>C | upstream_gene_variant | 0.15 | linezolid | |
rplC | 800654 | c.-155T>C | upstream_gene_variant | 0.18 | linezolid | |
rplC | 800759 | c.-50C>T | upstream_gene_variant | 0.15 | linezolid | |
rplC | 800762 | c.-47T>G | upstream_gene_variant | 0.14 | linezolid | |
fbiC | 1304817 | c.1887T>C | synonymous_variant | 0.18 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304826 | c.1896G>C | synonymous_variant | 0.18 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304829 | c.1899T>C | synonymous_variant | 0.19 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304832 | c.1902C>G | synonymous_variant | 0.19 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fbiC | 1304853 | c.1923C>T | synonymous_variant | 0.18 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304856 | c.1926C>G | synonymous_variant | 0.17 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304869 | c.1939C>T | synonymous_variant | 0.17 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1304874 | c.1944C>T | synonymous_variant | 0.17 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
sigE | 1364434 | p.Arg8Trp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471986 | n.141C>T | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472489 | n.644A>G | non_coding_transcript_exon_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473717 | n.60G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474552 | n.895C>T | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
linezolid | ||||||
rrl | 1474753 | n.1096A>G | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474830 | n.1173A>G | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475088 | n.1431A>G | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
linezolid | ||||||
rrl | 1475315 | n.1658A>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475480 | n.1823A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475532 | n.1875A>G | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475544 | n.1887A>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475707 | n.2050T>G | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.33 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.3 | 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 | 1476256 | n.2599A>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476583 | n.2926G>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rpsA | 1833829 | c.288A>G | synonymous_variant | 0.31 | pyrazinamide | |
rpsA | 1833832 | c.291G>A | synonymous_variant | 0.34 | pyrazinamide | |
rpsA | 1833838 | c.297G>C | synonymous_variant | 0.24 | pyrazinamide | |
rpsA | 1833841 | c.300C>G | synonymous_variant | 0.24 | pyrazinamide | |
rpsA | 1833847 | c.306C>G | synonymous_variant | 0.28 | pyrazinamide | |
rpsA | 1833856 | c.315A>G | synonymous_variant | 0.24 | pyrazinamide | |
rpsA | 1833862 | c.321G>T | synonymous_variant | 0.19 | pyrazinamide | |
rpsA | 1833892 | c.351G>A | synonymous_variant | 0.19 | pyrazinamide | |
rpsA | 1833894 | p.Ala118Glu | missense_variant | 0.19 | pyrazinamide | |
rpsA | 1833949 | c.408T>C | synonymous_variant | 0.19 | pyrazinamide | |
rpsA | 1834303 | c.762T>G | synonymous_variant | 0.23 | pyrazinamide | |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.23 | pyrazinamide | |
rpsA | 1834690 | c.1149T>C | synonymous_variant | 0.26 | pyrazinamide | |
rpsA | 1834732 | c.1191T>C | synonymous_variant | 0.35 | pyrazinamide | |
rpsA | 1834733 | p.Ala398Pro | missense_variant | 0.31 | pyrazinamide | |
rpsA | 1834738 | c.1197A>G | synonymous_variant | 0.33 | pyrazinamide | |
rpsA | 1834747 | c.1206A>G | synonymous_variant | 0.3 | pyrazinamide | |
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 |
Rv1979c | 2222854 | p.Ile104Thr | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2477c | 2782528 | c.1515G>T | synonymous_variant | 0.17 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2782537 | c.1506T>C | synonymous_variant | 0.13 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2782540 | c.1503T>C | synonymous_variant | 0.13 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.97 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3877593 | c.915C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3877602 | c.906C>T | synonymous_variant | 0.16 | rifampicin | |
rpoA | 3877608 | c.900G>A | synonymous_variant | 0.16 | rifampicin | |
rpoA | 3877656 | c.852T>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoA | 3877848 | c.660C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3877857 | c.651G>A | synonymous_variant | 0.17 | rifampicin | |
rpoA | 3877926 | c.582G>C | synonymous_variant | 0.2 | rifampicin | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.97 | pyrazinamide | Not assoc w R |
clpC1 | 4039226 | c.1479T>C | synonymous_variant | 0.16 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039241 | c.1464G>C | synonymous_variant | 0.21 | pyrazinamide | |
clpC1 | 4039517 | c.1188C>G | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039576 | p.Ala377Ser | missense_variant | 0.19 | pyrazinamide | |
clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4040411 | c.294T>C | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R - Interim |
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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |