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Detailed information for vg0807623757:

Variant ID: vg0807623757 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7623757
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.54, A: 0.44, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TCAATTAGGTGCGCCGCCAGCAAAAATTAGGTTGAATTTTTCCTGGCGACCAATAAACAGAACCGCCAGAGAAAACCCAACAAAAAAAATATCCTGTCAC[A/G]
TTAAAACACCCACCTACCTCATCCTCATCCTCTTCTTCACATTAAAACACCACACATCTCCCCTTCTTATCCACTCCTCTTCCCTCCTCCCTCTCCTCCT

Reverse complement sequence

AGGAGGAGAGGGAGGAGGGAAGAGGAGTGGATAAGAAGGGGAGATGTGTGGTGTTTTAATGTGAAGAAGAGGATGAGGATGAGGTAGGTGGGTGTTTTAA[T/C]
GTGACAGGATATTTTTTTTGTTGGGTTTTCTCTGGCGGTTCTGTTTATTGGTCGCCAGGAAAAATTCAACCTAATTTTTGCTGGCGGCGCACCTAATTGA

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 33.40% 31.50% 26.17% 8.91% NA
All Indica  2759 8.30% 42.50% 40.92% 8.30% NA
All Japonica  1512 82.90% 6.80% 1.19% 9.06% NA
Aus  269 17.10% 56.50% 26.39% 0.00% NA
Indica I  595 7.40% 19.20% 55.13% 18.32% NA
Indica II  465 9.50% 45.40% 39.78% 5.38% NA
Indica III  913 9.30% 51.40% 35.38% 3.94% NA
Indica Intermediate  786 7.00% 48.20% 37.28% 7.51% NA
Temperate Japonica  767 77.10% 6.00% 0.91% 16.04% NA
Tropical Japonica  504 93.30% 4.80% 0.60% 1.39% NA
Japonica Intermediate  241 80.10% 13.70% 3.32% 2.90% NA
VI/Aromatic  96 11.50% 32.30% 4.17% 52.08% NA
Intermediate  90 43.30% 34.40% 16.67% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807623757 A -> G LOC_Os08g12850.1 upstream_gene_variant ; 3465.0bp to feature; MODIFIER silent_mutation Average:72.32; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0807623757 A -> G LOC_Os08g12860.1 upstream_gene_variant ; 2555.0bp to feature; MODIFIER silent_mutation Average:72.32; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0807623757 A -> G LOC_Os08g12850-LOC_Os08g12860 intergenic_region ; MODIFIER silent_mutation Average:72.32; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0807623757 A -> DEL N N silent_mutation Average:72.32; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807623757 NA 1.39E-12 mr1010 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
vg0807623757 NA 4.05E-08 mr1162 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
vg0807623757 NA 2.57E-22 mr1548 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
vg0807623757 NA 1.28E-22 mr1588 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
vg0807623757 NA 4.81E-10 mr1630 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
vg0807623757 NA 1.15E-16 mr1842 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
vg0807623757 NA 3.52E-06 mr1080_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
vg0807623757 NA 1.87E-14 mr1162_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
vg0807623757 NA 8.88E-06 mr1203_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
vg0807623757 NA 1.66E-06 mr1458_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
vg0807623757 NA 3.48E-45 mr1486_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
vg0807623757 3.41E-06 7.63E-30 mr1588_2 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