Run ID: ERR11466444
Sample name:
Date: 2024-10-04T01:07:21.482428
Number of reads: 2027893
Percentage reads mapped: 99.0
Median coverage: 46.0
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 |
---|---|---|---|---|---|---|
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 | |||||
Rv0010c | 13483 | p.Ala26Thr | missense_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 761189 | c.1383T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 761198 | c.1392G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764662 | c.1293G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.14 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.98 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 775924 | c.2557C>T | synonymous_variant | 0.16 | bedaquiline | |
clofazimine | Not assoc w R - Interim | |||||
mmpL5 | 775937 | c.2544G>C | synonymous_variant | 0.2 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775949 | c.2532G>C | synonymous_variant | 0.17 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775961 | c.2520C>G | synonymous_variant | 0.22 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775975 | p.Leu836Met | missense_variant | 0.15 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 775981 | p.Leu834Met | missense_variant | 0.14 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 777212 | c.1269C>G | synonymous_variant | 0.14 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 777215 | c.1266C>G | synonymous_variant | 0.13 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
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 | 1472380 | n.535G>C | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472489 | n.644A>G | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474753 | n.1096A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475202 | n.1545G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1475206 | n.1549C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475209 | n.1552G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1475989 | n.2332T>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
linezolid | ||||||
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.36 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476032 | n.2375C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476033 | n.2376T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476034 | n.2377C>G | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476045 | n.2388G>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1833781 | c.240T>G | synonymous_variant | 0.11 | pyrazinamide | |
rpsA | 1833979 | c.438T>C | synonymous_variant | 0.11 | 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 | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | 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 | |||||
mtrB | 3625747 | c.867G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
mtrB | 3625755 | p.Ala287Thr | missense_variant | 0.15 | rifampicin | Uncertain significance |
bedaquiline | ||||||
lpqB | 3625762 | c.-852A>C | upstream_gene_variant | 0.14 | rifampicin | |
bedaquiline | ||||||
mtrB | 3625765 | p.Ser283Gln | missense_variant | 0.14 | rifampicin | |
bedaquiline | ||||||
lpqB | 3625795 | c.-885G>C | upstream_gene_variant | 0.17 | rifampicin | |
bedaquiline | ||||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | 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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |