Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1007764369:

Variant ID: vg1007764369 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7764369
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


AGAATTGTTGCTTTTGTCACAAAGATGAGACAATATTACATTTGTTTTATGAGTGCAGATTTGCCCGTTTTGTGTGGTGCATTATACAAGTGGCTACAGG[A/G]
CTTTTCCCGCCACGTGGTGTATCCAATATGTTTGGTAATTGGCTACGGGGAATTAAGAAAGACTTGAAGTCACTTATCCTGTTAGAGGCAGCCACTATTT

Reverse complement sequence

AAATAGTGGCTGCCTCTAACAGGATAAGTGACTTCAAGTCTTTCTTAATTCCCCGTAGCCAATTACCAAACATATTGGATACACCACGTGGCGGGAAAAG[T/C]
CCTGTAGCCACTTGTATAATGCACCACACAAAACGGGCAAATCTGCACTCATAAAACAAATGTAATATTGTCTCATCTTTGTGACAAAAGCAACAATTCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 20.60% 9.30% 22.51% 47.57% NA
All Indica  2759 9.20% 2.60% 23.81% 64.41% NA
All Japonica  1512 39.30% 23.90% 17.20% 19.64% NA
Aus  269 5.20% 0.40% 44.61% 49.81% NA
Indica I  595 17.00% 0.00% 22.02% 61.01% NA
Indica II  465 2.20% 3.20% 20.22% 74.41% NA
Indica III  913 5.00% 3.40% 28.59% 62.98% NA
Indica Intermediate  786 12.30% 3.20% 21.76% 62.72% NA
Temperate Japonica  767 53.10% 35.50% 5.35% 6.13% NA
Tropical Japonica  504 10.70% 13.30% 33.93% 42.06% NA
Japonica Intermediate  241 55.20% 9.10% 19.92% 15.77% NA
VI/Aromatic  96 85.40% 3.10% 10.42% 1.04% NA
Intermediate  90 32.20% 5.60% 18.89% 43.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007764369 A -> G LOC_Os10g14814.1 intron_variant ; MODIFIER silent_mutation Average:22.341; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1007764369 A -> DEL N N silent_mutation Average:22.341; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007764369 NA 6.76E-10 mr1026 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
vg1007764369 NA 3.09E-11 mr1118 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
vg1007764369 NA 4.37E-06 mr1130 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
vg1007764369 NA 4.76E-06 mr1256 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
vg1007764369 2.14E-06 2.14E-06 mr1394 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
vg1007764369 NA 1.64E-13 mr1495 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
vg1007764369 NA 2.69E-08 mr1496 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
vg1007764369 NA 6.10E-06 mr1789 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
vg1007764369 NA 1.10E-12 mr1495_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
vg1007764369 NA 1.30E-08 mr1709_2 Jap_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
vg1007764369 NA 8.65E-09 mr1768_2 Jap_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