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Detailed information for vg0808442319:

Variant ID: vg0808442319 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8442319
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAGAGATAAATGAGGAAAAATTTTGAAATGGGTGGGAGGGAAAATAGGGAATACTATTTTCGCGTGCGGCTCTCTTAATAGATACGCACGGGAAAATC[G/A]
GCTCATTTTCCCGTGCGGTCCGTTTAGGAGGACCGCACGAGAAAATCGATTTTCCCATACGGGCAACAGCCCAGCCCCGGTTCCCCTATTTTTCCGTGCA

Reverse complement sequence

TGCACGGAAAAATAGGGGAACCGGGGCTGGGCTGTTGCCCGTATGGGAAAATCGATTTTCTCGTGCGGTCCTCCTAAACGGACCGCACGGGAAAATGAGC[C/T]
GATTTTCCCGTGCGTATCTATTAAGAGAGCCGCACGCGAAAATAGTATTCCCTATTTTCCCTCCCACCCATTTCAAAATTTTTCCTCATTTATCTCTTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.80%	3.00%	0.21%	0.00%	NA
All Indica	2759	94.90%	5.00%	0.14%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	75.50%	24.10%	0.43%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	96.80%	3.10%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	1.10%	2.22%	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
vg0808442319	G -> A	LOC_Os08g14109.1	intron_variant ; MODIFIER	silent_mutation	Average:35.859; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808442319	2.02E-06	NA	mr1944_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