Search for Variation information by Variation ID:

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

Detailed information for vg0703430627:

Variant ID: vg0703430627 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3430627
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGAGAGATGAAAGGAGTCATTGCCAAGCATTGGAGAGAACAAAAGGGATGGTTTAAAGGGTGAACTAACTATCAACAGTCATCAAGGCTCTGTTACGT[G/A]
CCTTTGCTGCTCGTGTGAGACCCTTCCGAGAAATGTCAACACCGACAACTTTTTCAAGGGTTGTTGGATGCTCAAGCAATGAATCAAGAAGGCTACCAGA

Reverse complement sequence

TCTGGTAGCCTTCTTGATTCATTGCTTGAGCATCCAACAACCCTTGAAAAAGTTGTCGGTGTTGACATTTCTCGGAAGGGTCTCACACGAGCAGCAAAGG[C/T]
ACGTAACAGAGCCTTGATGACTGTTGATAGTTAGTTCACCCTTTAAACCATCCCTTTTGTTCTCTCCAATGCTTGGCAATGACTCCTTTCATCTCTCTGA

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 55.40% 44.20% 0.00% 0.38% NA
All Indica  2759 35.30% 64.10% 0.00% 0.54% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 84.90% 14.80% 0.00% 0.34% NA
Indica II  465 15.10% 84.30% 0.00% 0.65% NA
Indica III  913 15.40% 84.10% 0.00% 0.44% NA
Indica Intermediate  786 33.00% 66.30% 0.00% 0.76% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 55.60% 41.10% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0703430627 G -> DEL LOC_Os07g06970.1 N splice_donor_variant Average:57.215; most accessible tissue: Minghui63 flower, score: 73.71 N N N N
vg0703430627 G -> A LOC_Os07g06970.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:57.215; most accessible tissue: Minghui63 flower, score: 73.71 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0703430627 NA 1.76E-07 mr1291 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
vg0703430627 NA 8.78E-06 mr1679 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
vg0703430627 NA 7.83E-06 mr1904 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
vg0703430627 NA 2.38E-16 mr1557_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
vg0703430627 NA 4.79E-08 mr1659_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
vg0703430627 NA 1.07E-14 mr1767_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