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Detailed information for vg0410390630:

Variant ID: vg0410390630 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10390630
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TCTAAGTGATTTATACTATCTCGGCATGGCGACCGATCTATCCCGATCACTTGATTTAAGTATATATCGACATAAGGATTATATATTGTTAATATCTACA[G/A]
CCGATCGAGTAGATTTAGTTCTTTCTTATATATTCATGATTGCCGATCGATCCACATATGACATCGGCTCCGAGATAAATGATACGTCATCGGCAATTAG

Reverse complement sequence

CTAATTGCCGATGACGTATCATTTATCTCGGAGCCGATGTCATATGTGGATCGATCGGCAATCATGAATATATAAGAAAGAACTAAATCTACTCGATCGG[C/T]
TGTAGATATTAACAATATATAATCCTTATGTCGATATATACTTAAATCAAGTGATCGGGATAGATCGGTCGCCATGCCGAGATAGTATAAATCACTTAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 18.50% 5.37% 9.61% NA
All Indica  2759 48.90% 27.80% 8.55% 14.82% NA
All Japonica  1512 99.70% 0.20% 0.13% 0.00% NA
Aus  269 50.20% 30.90% 4.09% 14.87% NA
Indica I  595 22.90% 42.40% 18.49% 16.30% NA
Indica II  465 72.00% 16.60% 4.73% 6.67% NA
Indica III  913 51.50% 23.70% 6.02% 18.84% NA
Indica Intermediate  786 51.80% 28.10% 6.23% 13.87% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 10.40% 3.12% 4.17% NA
Intermediate  90 83.30% 13.30% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410390630 G -> DEL N N silent_mutation Average:7.345; most accessible tissue: Callus, score: 20.701 N N N N
vg0410390630 G -> A LOC_Os04g18730.1 intron_variant ; MODIFIER silent_mutation Average:7.345; most accessible tissue: Callus, score: 20.701 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410390630 NA 8.96E-06 mr1386 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 7.25E-06 mr1830 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 1.58E-08 mr1846 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 5.32E-06 mr1608_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 1.14E-06 mr1608_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 4.16E-07 mr1654_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 4.12E-07 mr1830_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 2.87E-14 mr1835_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 2.16E-08 mr1835_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0410390630 NA 4.38E-17 mr1846_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251