Run ID: SRR25827617
Sample name:
Date: 2024-04-16T01:46:58.493305
Number of reads: 5548222
Percentage reads mapped: 99.42
Median coverage: 62.0
Strain: lineage1.2.2.2;lineage2.2.1;lineage3
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.28 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.24 |
lineage2 | East-Asian | RD105 | 0.46 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.15 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.47 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.48 |
lineage1 | Indo-Oceanic | RD239 | 0.2 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
rrs | n.517C>T | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | c.589dupG | Assoc w R | |
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | mmpR5 | c.139dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.139dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.58 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.68 | rifampicin | Assoc w R | |
mmpR5 | 779127 | c.139dupG | frameshift_variant | 0.29 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.55 | streptomycin | Assoc w R | |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.4 | linezolid | Assoc w R | |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.37 | streptomycin | Assoc w R | |
tlyA | 1918524 | c.589dupG | frameshift_variant | 0.33 | capreomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.93 | isoniazid | Assoc w R | High-level resistance |
embB | 4247429 | p.Met306Val | missense_variant | 0.61 | ethambutol | Assoc w R |
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 | 8452 | p.Ala384Val | missense_variant | 0.35 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.3 | 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 | 13298 | p.Ile87Met | missense_variant | 0.17 | isoniazid | Not assoc w R |
fgd1 | 490977 | c.195C>G | synonymous_variant | 0.45 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.36 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620553 | c.663T>C | synonymous_variant | 0.32 | capreomycin | Not assoc w R |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.47 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.65 | ethionamide | Not assoc w R - Interim |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.27 | rifampicin | Not assoc w R |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.24 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.91 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.31 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.31 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.54 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.21 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.98 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.33 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
embR | 1416814 | c.534G>A | synonymous_variant | 0.15 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.37 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.62 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.5 | linezolid | Not assoc w R |
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 | 2102240 | p.Arg268His | missense_variant | 0.22 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
ndh | 2102359 | c.683delT | frameshift_variant | 0.34 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.96 | pyrazinamide | Not assoc w R |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.21 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.21 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2288683 | c.559T>G | stop_lost&splice_region_variant | 0.18 | pyrazinamide | Uncertain significance |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.26 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.29 | isoniazid | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.23 | isoniazid | Not assoc w R |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.54 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.3 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 0.31 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.44 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640211 | c.-332T>G | upstream_gene_variant | 0.42 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.38 | pyrazinamide | Not assoc w R - Interim |
panD | 4044023 | c.259C>T | synonymous_variant | 0.26 | pyrazinamide | Not assoc w R |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.19 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.16 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.5 | ethambutol | Not assoc w R |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.27 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.33 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.26 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.4 | ethambutol | Not assoc w R |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.55 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.33 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.2 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.26 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.45 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.3 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.23 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.88 | streptomycin | Not assoc w R |
gid | 4407848 | p.Ala119Thr | missense_variant | 0.39 | streptomycin | Uncertain significance |
gid | 4407873 | c.330G>T | synonymous_variant | 0.39 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.44 | streptomycin | Not assoc w R |