Run ID: ERR5866376
Sample name:
Date: 02-04-2023 00:39:16
Number of reads: 895853
Percentage reads mapped: 97.27
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.26 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.89 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7290 | c.-12A>G | upstream_gene_variant | 0.11 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8046 | p.Gly249Ser | missense_variant | 0.18 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575889 | p.Ala181Asp | missense_variant | 0.22 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.82 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
ccsA | 620757 | c.867C>T | synonymous_variant | 0.13 |
rpoB | 759711 | c.-95_-88delGCCGAAAC | upstream_gene_variant | 0.2 |
rpoB | 759723 | c.-84C>T | upstream_gene_variant | 0.2 |
rpoB | 759726 | c.-81A>T | upstream_gene_variant | 0.2 |
rpoB | 759727 | c.-80A>T | upstream_gene_variant | 0.2 |
rpoB | 759730 | c.-77A>G | upstream_gene_variant | 0.2 |
rpoB | 759733 | c.-74_-73insGTTTCGGC | upstream_gene_variant | 0.2 |
rpoB | 760688 | p.Phe294Leu | missense_variant | 0.14 |
rpoB | 761184 | p.Glu460Lys | missense_variant | 0.12 |
rpoC | 762962 | c.-408C>A | upstream_gene_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763630 | c.261G>C | synonymous_variant | 0.11 |
rpoC | 766334 | p.Val989Ile | missense_variant | 0.11 |
rpoC | 767273 | p.Gly1302Cys | missense_variant | 0.11 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.87 |
mmpL5 | 777170 | c.1311T>C | synonymous_variant | 0.14 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.89 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.96 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474469 | n.812T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474736 | n.1079C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476294 | n.2642delC | non_coding_transcript_exon_variant | 0.2 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 0.13 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918003 | p.Gln22Lys | missense_variant | 0.15 |
tlyA | 1918018 | p.Ile27Val | missense_variant | 1.0 |
ndh | 2101919 | p.Arg375Met | missense_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155789 | p.His108Arg | missense_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.96 |
Rv1979c | 2223180 | c.-16A>G | upstream_gene_variant | 0.1 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289071 | p.His57Gln | missense_variant | 1.0 |
kasA | 2519267 | p.Val385Ile | missense_variant | 0.12 |
eis | 2715332 | p.Val1Leu | missense_variant | 1.0 |
pepQ | 2859417 | c.1002C>A | synonymous_variant | 0.11 |
Rv2752c | 3064940 | c.1251delA | frameshift_variant | 0.14 |
Rv2752c | 3065518 | p.Leu225Pro | missense_variant | 1.0 |
Rv2752c | 3066146 | c.45delG | frameshift_variant | 0.12 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612288 | p.Gly277Arg | missense_variant | 0.18 |
Rv3236c | 3612805 | c.311delG | frameshift_variant | 0.17 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642018 | c.485_489delATGCC | frameshift_variant | 0.18 |
fbiB | 3642027 | c.494delT | frameshift_variant | 0.18 |
fbiB | 3642031 | p.Gly166Ala | missense_variant | 0.18 |
fbiB | 3642033 | c.499_500insA | frameshift_variant | 0.18 |
fbiB | 3642037 | c.503_504insGGCAT | frameshift_variant | 0.18 |
fbiB | 3642563 | p.Asp343Glu | missense_variant | 0.25 |
rpoA | 3877969 | p.Ala180Gly | missense_variant | 0.96 |
clpC1 | 4039162 | p.His515Asp | missense_variant | 0.1 |
embA | 4242325 | c.-908C>A | upstream_gene_variant | 0.5 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243641 | c.414_415dupGC | frameshift_variant | 0.13 |
embA | 4243835 | c.603G>A | synonymous_variant | 0.11 |
embA | 4245997 | p.Trp922Ser | missense_variant | 0.11 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ubiA | 4269941 | c.-108C>A | upstream_gene_variant | 0.15 |
ubiA | 4270026 | c.-193C>G | upstream_gene_variant | 0.2 |
ethA | 4326049 | c.1425C>T | synonymous_variant | 0.13 |
ethA | 4326155 | p.Leu440Pro | missense_variant | 1.0 |
ethR | 4327060 | c.-489G>A | upstream_gene_variant | 0.11 |
ethR | 4327940 | p.Ser131Thr | missense_variant | 0.1 |
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 |