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Detailed information for vg0322966434:

Variant ID: vg0322966434 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22966434
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTGCAAATGCACAAATCATAGAAAAATATTTTTTACTAACATAAAATTTTAAAAATTATTAAAGACAAATAGAAGTGCACAGTAGCGTTTAGCACGGG[G/A]
CATATTACTAGTAGGGTAGATTTAAAAACTGAGGTGCTTACTTTTCTCTGGAGCTATATCTGTTTGACACACTTCAACTAGATTGGTTATTATCAAAAAA

Reverse complement sequence

TTTTTTGATAATAACCAATCTAGTTGAAGTGTGTCAAACAGATATAGCTCCAGAGAAAAGTAAGCACCTCAGTTTTTAAATCTACCCTACTAGTAATATG[C/T]
CCCGTGCTAAACGCTACTGTGCACTTCTATTTGTCTTTAATAATTTTTAAAATTTTATGTTAGTAAAAAATATTTTTCTATGATTTGTGCATTTGCACTT

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	55.20%	44.30%	0.30%	0.21%	NA
All Indica	2759	91.30%	8.10%	0.29%	0.36%	NA
All Japonica	1512	0.70%	99.10%	0.13%	0.00%	NA
Aus	269	14.90%	85.10%	0.00%	0.00%	NA
Indica I	595	97.00%	2.70%	0.34%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	89.70%	9.70%	0.22%	0.33%	NA
Indica Intermediate	786	85.20%	13.50%	0.38%	0.89%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.60%	0.20%	0.00%	NA
Japonica Intermediate	241	0.40%	99.20%	0.41%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	40.00%	55.60%	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
vg0322966434	G -> A	LOC_Os03g41310.1	downstream_gene_variant ; 2821.0bp to feature; MODIFIER	silent_mutation	Average:42.47; most accessible tissue: Callus, score: 74.86	N	N	N	N
vg0322966434	G -> A	LOC_Os03g41300.1	intron_variant ; MODIFIER	silent_mutation	Average:42.47; most accessible tissue: Callus, score: 74.86	N	N	N	N
vg0322966434	G -> DEL	N	N	silent_mutation	Average:42.47; most accessible tissue: Callus, score: 74.86	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322966434	NA	1.67E-57	mr1526_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
vg0322966434	7.58E-07	NA	mr1750_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
vg0322966434	3.45E-10	NA	mr1750_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