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Detailed information for vg0301312981:

Variant ID: vg0301312981 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1312981
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAGGATACAAGTGTAGTGTGAAAATAGGACCCCTAAACTTCTTCATAAAATTACCATAAAGGTGTCTCATGCACTCCCTATGTTCAGCTTTCTCAAAT[G/A]
CAGCACCTACAGCTTTCTCTAGCCCTTTGCATGCATCTGTTGATATGACTAACCTTTCAGGAGCACCTATAGCTCCATGCAACTGTTTCATAAACCACAA

Reverse complement sequence

TTGTGGTTTATGAAACAGTTGCATGGAGCTATAGGTGCTCCTGAAAGGTTAGTCATATCAACAGATGCATGCAAAGGGCTAGAGAAAGCTGTAGGTGCTG[C/T]
ATTTGAGAAAGCTGAACATAGGGAGTGCATGAGACACCTTTATGGTAATTTTATGAAGAAGTTTAGGGGTCCTATTTTCACACTACACTTGTATCCTGCT

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	37.40%	0.90%	14.94%	46.76%	NA
All Indica	2759	4.50%	1.20%	19.54%	74.74%	NA
All Japonica	1512	99.30%	0.00%	0.60%	0.13%	NA
Aus	269	17.80%	1.50%	48.70%	31.97%	NA
Indica I	595	3.20%	1.80%	16.30%	78.66%	NA
Indica II	465	7.30%	1.90%	33.55%	57.20%	NA
Indica III	913	3.00%	0.50%	10.08%	86.42%	NA
Indica Intermediate	786	5.70%	1.00%	24.68%	68.58%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.79%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	49.00%	2.10%	13.54%	35.42%	NA
Intermediate	90	52.20%	3.30%	15.56%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301312981	G -> A	LOC_Os03g03120.1	missense_variant ; p.Ala517Val; MODERATE	nonsynonymous_codon ; A517V	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	unknown	unknown	TOLERATED	1.00
vg0301312981	G -> DEL	LOC_Os03g03120.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301312981	NA	4.53E-15	mr1361	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
vg0301312981	7.56E-06	NA	mr1379	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
vg0301312981	NA	6.50E-06	mr1516	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
vg0301312981	NA	4.91E-09	mr1575	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
vg0301312981	NA	1.66E-12	mr1377_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