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Detailed information for vg0802712498:

Variant ID: vg0802712498 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2712498
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, A: 0.39, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

GACCCCGGGTGTACATATTTATACCCATGGTTGATACAAGTCCTTGTCGGACAAGAAAGAAACTATCCTAAAGATAAAAGGAAAACATAAAGTCCTTATC[A/G]
GACACTAAACACACTTTCCTAAAGATAAAAGGGAACTAACAAACTATTCATAATTAATAGATAAACTGCCATGCCACATCCTCTTTGAACTCGGTTGCTT

Reverse complement sequence

AAGCAACCGAGTTCAAAGAGGATGTGGCATGGCAGTTTATCTATTAATTATGAATAGTTTGTTAGTTCCCTTTTATCTTTAGGAAAGTGTGTTTAGTGTC[T/C]
GATAAGGACTTTATGTTTTCCTTTTATCTTTAGGATAGTTTCTTTCTTGTCCGACAAGGACTTGTATCAACCATGGGTATAAATATGTACACCCGGGGTC

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	66.90%	21.40%	6.98%	4.72%	NA
All Indica	2759	55.10%	27.00%	10.91%	7.00%	NA
All Japonica	1512	97.90%	0.40%	1.12%	0.53%	NA
Aus	269	1.50%	87.70%	3.72%	7.06%	NA
Indica I	595	75.50%	2.20%	15.29%	7.06%	NA
Indica II	465	67.70%	13.80%	9.03%	9.46%	NA
Indica III	913	37.20%	46.00%	10.73%	6.02%	NA
Indica Intermediate	786	52.80%	31.70%	8.91%	6.62%	NA
Temperate Japonica	767	99.30%	0.30%	0.13%	0.26%	NA
Tropical Japonica	504	95.00%	0.80%	2.98%	1.19%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	9.40%	0.00%	2.08%	NA
Intermediate	90	78.90%	17.80%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0802712498	A -> G	LOC_Os08g05220.1	downstream_gene_variant ; 2050.0bp to feature; MODIFIER	silent_mutation	Average:41.937; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N
vg0802712498	A -> G	LOC_Os08g05210.1	intron_variant ; MODIFIER	silent_mutation	Average:41.937; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N
vg0802712498	A -> DEL	N	N	silent_mutation	Average:41.937; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802712498	9.02E-07	5.76E-10	Heading_date	Ind_All	YES	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
vg0802712498	NA	3.52E-06	mr1004	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
vg0802712498	NA	5.78E-06	mr1052	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
vg0802712498	NA	1.09E-07	mr1066	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
vg0802712498	NA	3.07E-06	mr1192	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
vg0802712498	NA	1.67E-06	mr1556	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
vg0802712498	NA	4.39E-08	mr1510_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