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Detailed information for vg0431121130:

Variant ID: vg0431121130 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31121130
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCTCTCTCTTGAATAATGTAGCTGGCAGCCTGGCACTAGATTTTTTGTAAACATATAGACATATTACAAATTAGATATACCACTAGAATAGAAAAGGA[G/A]
CATACATGATGAGATTGGTTTCTTGCAGTGTGCAGGTCTTCCATTTTCCTCTTATTTTGTATCATTACACAATTAGTAACATCTCCAGATTCAAGATACC

Reverse complement sequence

GGTATCTTGAATCTGGAGATGTTACTAATTGTGTAATGATACAAAATAAGAGGAAAATGGAAGACCTGCACACTGCAAGAAACCAATCTCATCATGTATG[C/T]
TCCTTTTCTATTCTAGTGGTATATCTAATTTGTAATATGTCTATATGTTTACAAAAAATCTAGTGCCAGGCTGCCAGCTACATTATTCAAGAGAGAGAGT

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	57.80%	42.00%	0.19%	0.00%	NA
All Indica	2759	87.50%	12.30%	0.25%	0.00%	NA
All Japonica	1512	4.70%	95.30%	0.00%	0.00%	NA
Aus	269	43.90%	55.40%	0.74%	0.00%	NA
Indica I	595	80.30%	18.80%	0.84%	0.00%	NA
Indica II	465	84.10%	15.90%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	81.40%	18.30%	0.25%	0.00%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.40%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	90.00%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	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
vg0431121130	G -> A	LOC_Os04g52380.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:43.198; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0431121130	G -> A	LOC_Os04g52380.2	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:43.198; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0431121130	G -> A	LOC_Os04g52380.3	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:43.198; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0431121130	G -> A	LOC_Os04g52380.4	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:43.198; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431121130	NA	4.54E-07	mr1629_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