Run ID: ERR8665589
Sample name:
Date: 02-04-2023 07:32:56
Number of reads: 493433
Percentage reads mapped: 99.57
Strain: lineage2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
tlyA | 1918517 | c.582delC | frameshift_variant | 1.0 | capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288756 | c.484_485dupGG | frameshift_variant | 1.0 | pyrazinamide |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6539 | p.Asp434Asn | missense_variant | 0.15 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9189 | p.Gly630Trp | missense_variant | 0.25 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9309 | p.Asp670Tyr | missense_variant | 0.5 |
fgd1 | 490941 | p.Phe53Leu | missense_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575474 | p.Asp43Tyr | missense_variant | 0.22 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576291 | p.Leu315Pro | missense_variant | 0.22 |
ccsA | 619795 | c.-96C>T | upstream_gene_variant | 0.4 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
ccsA | 620661 | c.771C>A | synonymous_variant | 0.2 |
rpoB | 760777 | p.Ser324* | stop_gained | 0.25 |
rpoB | 761561 | c.1755C>A | synonymous_variant | 0.25 |
rpoB | 762144 | p.Glu780* | stop_gained | 0.17 |
rpoB | 762477 | p.Lys891Glu | missense_variant | 1.0 |
rpoB | 762915 | p.Ala1037Thr | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763289 | c.-81C>A | upstream_gene_variant | 0.18 |
rpoC | 765139 | c.1770C>A | synonymous_variant | 0.23 |
rpoC | 765848 | p.Pro827Thr | missense_variant | 0.2 |
rpoC | 766552 | p.Phe1061Leu | missense_variant | 0.12 |
rpoC | 767111 | p.Leu1248Met | missense_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775778 | c.2703C>A | synonymous_variant | 0.22 |
mmpL5 | 775781 | c.2700G>T | synonymous_variant | 0.2 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776124 | p.Leu786Pro | missense_variant | 0.12 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776666 | p.Asp605Glu | missense_variant | 0.12 |
mmpL5 | 778678 | c.-198C>A | upstream_gene_variant | 0.25 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781501 | c.-59C>A | upstream_gene_variant | 0.2 |
fbiC | 1303702 | p.Gly258Cys | missense_variant | 0.18 |
fbiC | 1304348 | p.Trp473Leu | missense_variant | 0.29 |
fbiC | 1305014 | p.Thr695Met | missense_variant | 0.18 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
Rv1258c | 1406887 | p.Leu152Met | missense_variant | 0.13 |
Rv1258c | 1406915 | c.426C>A | synonymous_variant | 0.2 |
Rv1258c | 1406978 | p.Met121Ile | missense_variant | 0.25 |
embR | 1416791 | p.Arg186Leu | missense_variant | 0.25 |
atpE | 1461134 | c.90C>A | synonymous_variant | 0.19 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474644 | n.987G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476310 | n.2653G>T | non_coding_transcript_exon_variant | 0.15 |
fabG1 | 1673887 | p.Gln150Glu | missense_variant | 0.12 |
inhA | 1674147 | c.-55C>A | upstream_gene_variant | 0.2 |
inhA | 1674420 | p.Ser73Arg | missense_variant | 0.17 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834291 | p.Glu250Asp | missense_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102245 | c.798C>A | synonymous_variant | 0.17 |
ndh | 2102253 | p.Gly264Ser | missense_variant | 0.17 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169912 | p.Asn234Ser | missense_variant | 0.22 |
PPE35 | 2169953 | c.660C>A | synonymous_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518501 | p.Met129Ile | missense_variant | 0.18 |
folC | 2746857 | p.Glu248* | stop_gained | 0.4 |
folC | 2746930 | c.669C>A | synonymous_variant | 0.25 |
pepQ | 2859573 | c.846C>A | synonymous_variant | 0.29 |
ribD | 2986985 | p.Leu49Phe | missense_variant | 0.29 |
Rv2752c | 3064673 | p.Ala507Thr | missense_variant | 0.14 |
Rv2752c | 3065398 | p.Ser265* | stop_gained | 0.18 |
Rv2752c | 3065453 | p.Gln247* | stop_gained | 1.0 |
Rv2752c | 3066083 | p.Leu37Met | missense_variant | 0.18 |
Rv2752c | 3066127 | p.Gly22Val | missense_variant | 0.12 |
Rv2752c | 3066258 | c.-67G>T | upstream_gene_variant | 0.17 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448861 | p.Gly120Cys | missense_variant | 0.18 |
Rv3083 | 3449183 | p.Ser227Tyr | missense_variant | 0.22 |
Rv3083 | 3449537 | p.Ala345Val | missense_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568736 | c.-57T>G | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3641499 | p.Met319Ile | missense_variant | 0.29 |
fbiB | 3641724 | p.Pro64Thr | missense_variant | 0.29 |
alr | 3840349 | p.Ala358Thr | missense_variant | 0.14 |
ddn | 3986886 | p.Asp15Tyr | missense_variant | 0.25 |
clpC1 | 4039180 | c.1524delG | frameshift_variant | 0.18 |
clpC1 | 4039586 | c.1119G>T | synonymous_variant | 0.22 |
clpC1 | 4040165 | c.540G>T | synonymous_variant | 0.22 |
clpC1 | 4040633 | p.Asn24Lys | missense_variant | 0.13 |
embC | 4239711 | c.-152C>A | upstream_gene_variant | 0.2 |
embC | 4241386 | c.1524C>G | synonymous_variant | 0.17 |
embC | 4241611 | c.1749G>T | synonymous_variant | 0.18 |
embC | 4241937 | p.Arg692Met | missense_variant | 0.22 |
embA | 4242367 | c.-866C>A | upstream_gene_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243355 | c.123G>T | synonymous_variant | 0.22 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245343 | p.Ser704* | stop_gained | 0.2 |
embA | 4245878 | p.Glu882Asp | missense_variant | 0.18 |
embA | 4245975 | p.Asp915Tyr | missense_variant | 0.29 |
embB | 4246310 | c.-204C>A | upstream_gene_variant | 0.17 |
embA | 4246317 | p.Pro1029Thr | missense_variant | 0.15 |
embB | 4247083 | c.570C>A | synonymous_variant | 0.15 |
embB | 4247132 | p.Asp207Tyr | missense_variant | 0.2 |
embB | 4248939 | p.Pro809His | missense_variant | 0.15 |
aftB | 4267576 | p.Ala421Ser | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268013 | p.Pro275Gln | missense_variant | 0.18 |
ubiA | 4269426 | p.Leu136Phe | missense_variant | 0.17 |
aftB | 4269576 | c.-740C>A | upstream_gene_variant | 0.25 |
ethA | 4326031 | c.1443C>A | synonymous_variant | 0.15 |
ethA | 4326851 | p.Ser208Leu | missense_variant | 1.0 |
ethA | 4326927 | p.Ser183Arg | missense_variant | 0.37 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |