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Detailed information for vg0314425542:

Variant ID: vg0314425542 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14425542
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, G: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTGATTATTGCTCCAATGTTAAGGGCCACACATTGCAGGTTTTGTTTGTGTTAAAATAGAGCAATTGAAAGGATTGGGCCATCTTGACCGGTAGTTTT[A/G]
GTAAATGACCTCTGCAGATGTTTGCATGAAGAGTTTTGTGTAGAATTTCTACTGCTCATATATGTGGCGAATATGCTCTGCCTTAATTATACCAGCACTA

Reverse complement sequence

TAGTGCTGGTATAATTAAGGCAGAGCATATTCGCCACATATATGAGCAGTAGAAATTCTACACAAAACTCTTCATGCAAACATCTGCAGAGGTCATTTAC[T/C]
AAAACTACCGGTCAAGATGGCCCAATCCTTTCAATTGCTCTATTTTAACACAAACAAAACCTGCAATGTGTGGCCCTTAACATTGGAGCAATAATCAAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.30%	39.60%	0.11%	0.00%	NA
All Indica	2759	80.10%	19.80%	0.14%	0.00%	NA
All Japonica	1512	33.40%	66.60%	0.00%	0.00%	NA
Aus	269	30.50%	69.10%	0.37%	0.00%	NA
Indica I	595	81.00%	18.50%	0.50%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	73.50%	26.50%	0.00%	0.00%	NA
Indica Intermediate	786	77.00%	22.90%	0.13%	0.00%	NA
Temperate Japonica	767	60.90%	39.10%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	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
vg0314425542	A -> G	LOC_Os03g25250.1	upstream_gene_variant ; 1211.0bp to feature; MODIFIER	silent_mutation	Average:45.183; most accessible tissue: Callus, score: 81.119	N	N	N	N
vg0314425542	A -> G	LOC_Os03g25260.1	intron_variant ; MODIFIER	silent_mutation	Average:45.183; most accessible tissue: Callus, score: 81.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314425542	NA	7.40E-21	Plant_height	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
vg0314425542	NA	1.74E-12	Plant_height	Jap_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
vg0314425542	NA	1.97E-09	mr1037	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
vg0314425542	NA	9.73E-09	mr1137	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
vg0314425542	NA	3.90E-06	mr1155	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
vg0314425542	NA	2.95E-11	mr1486	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
vg0314425542	NA	2.88E-08	mr1548	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
vg0314425542	NA	9.18E-06	mr1561	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
vg0314425542	NA	6.01E-08	mr1617	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
vg0314425542	NA	3.79E-06	mr1729	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
vg0314425542	1.56E-06	1.43E-12	mr1798	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
vg0314425542	NA	4.51E-06	mr1037_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
vg0314425542	NA	7.73E-08	mr1137_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
vg0314425542	NA	7.82E-09	mr1319_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
vg0314425542	NA	1.83E-06	mr1380_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
vg0314425542	NA	6.36E-12	mr1486_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
vg0314425542	NA	8.42E-07	mr1561_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
vg0314425542	NA	3.39E-08	mr1588_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
vg0314425542	NA	4.36E-15	mr1798_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
vg0314425542	NA	2.09E-07	mr1996_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