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Detailed information for vg0314131280:

Variant ID: vg0314131280 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14131280
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATAAAGAGGCATGGGGACGTCGCTTGCCGTTGTCAGGCCGCTGATCATTAATTGGCCGACGCGGCGCTCCACGGTGGCGTCACTCAAGCCTGCAGATC[A/G]
AGAACAGAATTCGATAAATTAGGGAGAACATGCACAGAAGGGGATCAAATTAAACACAAGAAAAATACCCCGAGGAGAAACCCGGGTCGCGTCCTCCGGC

Reverse complement sequence

GCCGGAGGACGCGACCCGGGTTTCTCCTCGGGGTATTTTTCTTGTGTTTAATTTGATCCCCTTCTGTGCATGTTCTCCCTAATTTATCGAATTCTGTTCT[T/C]
GATCTGCAGGCTTGAGTGACGCCACCGTGGAGCGCCGCGTCGGCCAATTAATGATCAGCGGCCTGACAACGGCAAGCGACGTCCCCATGCCTCTTTATGA

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 35.10% 28.40% 9.01% 27.51% NA
All Indica  2759 4.30% 47.30% 8.30% 40.05% NA
All Japonica  1512 93.50% 0.20% 0.73% 5.56% NA
Aus  269 5.20% 4.10% 59.11% 31.60% NA
Indica I  595 7.60% 22.00% 4.03% 66.39% NA
Indica II  465 4.90% 28.80% 10.54% 55.70% NA
Indica III  913 0.80% 79.80% 8.54% 10.84% NA
Indica Intermediate  786 5.60% 39.70% 9.92% 44.78% NA
Temperate Japonica  767 91.50% 0.10% 0.13% 8.21% NA
Tropical Japonica  504 95.20% 0.20% 1.39% 3.17% NA
Japonica Intermediate  241 96.30% 0.40% 1.24% 2.07% NA
VI/Aromatic  96 72.90% 1.00% 18.75% 7.29% NA
Intermediate  90 46.70% 22.20% 10.00% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314131280 A -> DEL N N silent_mutation Average:11.573; most accessible tissue: Callus, score: 43.229 N N N N
vg0314131280 A -> G LOC_Os03g24790.1 downstream_gene_variant ; 2976.0bp to feature; MODIFIER silent_mutation Average:11.573; most accessible tissue: Callus, score: 43.229 N N N N
vg0314131280 A -> G LOC_Os03g24800.1 intron_variant ; MODIFIER silent_mutation Average:11.573; most accessible tissue: Callus, score: 43.229 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314131280 NA 8.61E-11 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314131280 NA 1.64E-08 mr1005 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
vg0314131280 NA 1.66E-12 mr1322 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
vg0314131280 NA 4.40E-06 mr1425 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
vg0314131280 NA 9.06E-09 mr1527 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
vg0314131280 NA 4.87E-09 mr1532 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
vg0314131280 NA 4.32E-06 mr1574 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
vg0314131280 NA 4.42E-12 mr1623 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
vg0314131280 NA 1.30E-09 mr1730 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
vg0314131280 NA 1.29E-21 mr1817 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
vg0314131280 NA 9.43E-09 mr1002_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
vg0314131280 NA 3.91E-06 mr1020_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
vg0314131280 NA 5.50E-17 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
vg0314131280 NA 8.31E-08 mr1170_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
vg0314131280 NA 1.27E-09 mr1349_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
vg0314131280 NA 1.04E-06 mr1452_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
vg0314131280 NA 9.54E-07 mr1568_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
vg0314131280 NA 1.71E-08 mr1576_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
vg0314131280 NA 2.91E-10 mr1749_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
vg0314131280 NA 3.82E-06 mr1754_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
vg0314131280 NA 4.63E-10 mr1761_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
vg0314131280 NA 2.63E-09 mr1821_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
vg0314131280 NA 1.68E-07 mr1882_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
vg0314131280 NA 8.21E-11 mr1893_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