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Detailed information for vg0314719214:

Variant ID: vg0314719214 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14719214
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCCCGTACGTTTGCCAAAGCAAATCTCCCCATCAAATCCGGCCGAATCTTTCTTGGGTAACCAAAATTGTTCAAGGTTTTTGATCCACTCGATCTACT[C/A]
TTTCCGTTTTCCCCAAAATCAGAGCGTAAAATTCGGGATAAAAATGACCGGGGAAGATCGCCGTCAAAATCGGCAACTTTAGAACAGAGATTAAATCCAG

Reverse complement sequence

CTGGATTTAATCTCTGTTCTAAAGTTGCCGATTTTGACGGCGATCTTCCCCGGTCATTTTTATCCCGAATTTTACGCTCTGATTTTGGGGAAAACGGAAA[G/T]
AGTAGATCGAGTGGATCAAAAACCTTGAACAATTTTGGTTACCCAAGAAAGATTCGGCCGGATTTGATGGGGAGATTTGCTTTGGCAAACGTACGGGCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.10%	22.30%	0.66%	0.00%	NA
All Indica	2759	61.60%	37.40%	0.98%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	61.30%	37.00%	1.68%	0.00%	NA
Indica II	465	80.60%	17.80%	1.51%	0.00%	NA
Indica III	913	49.20%	50.40%	0.44%	0.00%	NA
Indica Intermediate	786	64.90%	34.40%	0.76%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	83.30%	14.40%	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
vg0314719214	C -> A	LOC_Os03g25710.1	synonymous_variant ; p.Leu369Leu; LOW	synonymous_codon	Average:36.715; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314719214	1.20E-11	NA	mr1542	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
vg0314719214	3.46E-09	3.34E-18	mr1542	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
vg0314719214	6.01E-09	NA	mr1542_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
vg0314719214	1.22E-08	1.86E-16	mr1542_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