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Detailed information for vg0609007802:

Variant ID: vg0609007802 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9007802
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CATCTCCACTTTCCTCCTCGCTAGCCCCCTCAACATTGGCCTCAACCTCTTCATCACTTTGAGCGTAATCCTCTCTGCTCGATTCCTCAGGCTCACTCAC[G/A]
GGATCAGGCGCACGACGACCATGACGAGTGCGGGGAGGCATCACTGAAAAAATAGGAGCAAAGGATATATAAGCAATAATTTTAGAAACCACATAGTGAA

Reverse complement sequence

TTCACTATGTGGTTTCTAAAATTATTGCTTATATATCCTTTGCTCCTATTTTTTCAGTGATGCCTCCCCGCACTCGTCATGGTCGTCGTGCGCCTGATCC[C/T]
GTGAGTGAGCCTGAGGAATCGAGCAGAGAGGATTACGCTCAAAGTGATGAAGAGGTTGAGGCCAATGTTGAGGGGGCTAGCGAGGAGGAAAGTGGAGATG

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 77.80% 22.10% 0.06% 0.00% NA
All Indica  2759 91.60% 8.40% 0.00% 0.00% NA
All Japonica  1512 49.30% 50.50% 0.20% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 83.00% 17.00% 0.00% 0.00% NA
Indica III  913 95.00% 5.00% 0.00% 0.00% NA
Indica Intermediate  786 89.40% 10.60% 0.00% 0.00% NA
Temperate Japonica  767 76.00% 23.70% 0.26% 0.00% NA
Tropical Japonica  504 15.90% 83.90% 0.20% 0.00% NA
Japonica Intermediate  241 34.40% 65.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609007802 G -> A LOC_Os06g15860.1 synonymous_variant ; p.Pro14Pro; LOW synonymous_codon Average:67.737; most accessible tissue: Minghui63 young leaf, score: 79.896 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609007802 NA 1.43E-06 mr1087 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
vg0609007802 NA 3.15E-06 mr1242 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
vg0609007802 2.98E-07 NA mr1842 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
vg0609007802 NA 6.64E-12 mr1871 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
vg0609007802 2.32E-06 1.40E-12 mr1087_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
vg0609007802 NA 3.14E-06 mr1091_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
vg0609007802 NA 6.04E-07 mr1096_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
vg0609007802 NA 8.52E-10 mr1570_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