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

Detailed information for vg0800345996:

Variant ID: vg0800345996 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 345996
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCCTGGTGGTTCCATGGGCTACAAGGCTACCCAACAAGTTAAACAAGCTAAAAGGGTCACTACGCAGTCTCACCATACTATTCAATCCCCCGGATGCG[T/G]
TAGGCATGGAGGCCATTGGTGAGCTGAAAAATCTAAGGGACCTAAACATCTCTGTTAACAGGTGGCGGGACGATGAGATCCTTAGCCTTTATGCTCTGGG

Reverse complement sequence

CCCAGAGCATAAAGGCTAAGGATCTCATCGTCCCGCCACCTGTTAACAGAGATGTTTAGGTCCCTTAGATTTTTCAGCTCACCAATGGCCTCCATGCCTA[A/C]
CGCATCCGGGGGATTGAATAGTATGGTGAGACTGCGTAGTGACCCTTTTAGCTTGTTTAACTTGTTGGGTAGCCTTGTAGCCCATGGAACCACCAGGGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.30% 37.70% 0.00% 0.00% NA
All Indica  2759 88.90% 11.10% 0.00% 0.00% NA
All Japonica  1512 13.40% 86.60% 0.00% 0.00% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 80.40% 19.60% 0.00% 0.00% NA
Indica III  913 88.50% 11.50% 0.00% 0.00% NA
Indica Intermediate  786 86.10% 13.90% 0.00% 0.00% NA
Temperate Japonica  767 2.70% 97.30% 0.00% 0.00% NA
Tropical Japonica  504 30.60% 69.40% 0.00% 0.00% NA
Japonica Intermediate  241 11.60% 88.40% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0800345996 T -> G LOC_Os08g01580.1 missense_variant ; p.Leu695Val; MODERATE nonsynonymous_codon ; L695V Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown TOLERATED 0.55

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800345996 NA 2.23E-11 mr1277 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
vg0800345996 NA 3.70E-06 mr1364 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
vg0800345996 NA 1.46E-06 mr1443 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
vg0800345996 1.05E-06 3.82E-20 mr1746 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
vg0800345996 8.97E-06 1.01E-07 mr1746 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
vg0800345996 NA 3.77E-12 mr1746 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
vg0800345996 NA 4.74E-16 mr1277_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
vg0800345996 NA 2.00E-06 mr1558_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
vg0800345996 6.04E-10 1.91E-32 mr1746_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
vg0800345996 1.04E-07 8.06E-11 mr1746_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
vg0800345996 1.84E-07 1.20E-13 mr1746_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