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Detailed information for vg0404263841:

Variant ID: vg0404263841 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4263841
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAGGACACGTTGCCAACTATGTTCCTGATGAAAGACATGTTGCTGCTGCTTCCTATGCCTATGGTGTTGATACCACTTGGTATATAGACATTAGGGCA[A/G]
CAGATCATCTCACAAGTGAATTGGACAAATTGACTACTCGAGAGAAGTACAAGGGCACCGATCAGATTCACACCGCCAGTGGCGCAGGTATGAAAATTAA

Reverse complement sequence

TTAATTTTCATACCTGCGCCACTGGCGGTGTGAATCTGATCGGTGCCCTTGTACTTCTCTCGAGTAGTCAATTTGTCCAATTCACTTGTGAGATGATCTG[T/C]
TGCCCTAATGTCTATATACCAAGTGGTATCAACACCATAGGCATAGGAAGCAGCAGCAACATGTCTTTCATCAGGAACATAGTTGGCAACGTGTCCTCTT

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	75.90%	22.30%	1.76%	0.02%	NA
All Indica	2759	67.70%	31.80%	0.54%	0.00%	NA
All Japonica	1512	92.30%	7.50%	0.20%	0.00%	NA
Aus	269	58.70%	18.60%	22.30%	0.37%	NA
Indica I	595	96.00%	4.00%	0.00%	0.00%	NA
Indica II	465	81.70%	18.30%	0.00%	0.00%	NA
Indica III	913	40.50%	58.60%	0.88%	0.00%	NA
Indica Intermediate	786	69.60%	29.50%	0.89%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	79.60%	20.40%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	4.60%	1.24%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	83.30%	12.20%	4.44%	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
vg0404263841	A -> DEL	N	N	silent_mutation	Average:62.044; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0404263841	A -> G	LOC_Os04g07990-LOC_Os04g08010	intergenic_region ; MODIFIER	silent_mutation	Average:62.044; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404263841	NA	6.51E-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
vg0404263841	1.50E-06	2.58E-06	mr1136_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
vg0404263841	NA	7.31E-06	mr1457_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
vg0404263841	1.57E-06	1.57E-06	mr1574_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