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Detailed information for vg0321809345:

Variant ID: vg0321809345 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21809345
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TCCATCTTAGGGAACACTGTAGCTCCTTTCAACTGATCAAACAGATCATCAATCCTTGACAAAGGGTACTTGTTCTTAATAGTGACCTCATTGAGTGCGT[A/G]
CTAGTTAACGCACATCCTCTTGGTTTTGTCTTTCTTTTCCACAAAGATTACCGGAGCACCCCAAGGCAACGTGCTCGGGCGAATGTATCCCTTCTGTAAC

Reverse complement sequence

GTTACAGAAGGGATACATTCGCCCGAGCACGTTGCCTTGGGGTGCTCCGGTAATCTTTGTGGAAAAGAAAGACAAAACCAAGAGGATGTGCGTTAACTAG[T/C]
ACGCACTCAATGAGGTCACTATTAAGAACAAGTACCCTTTGTCAAGGATTGATGATCTGTTTGATCAGTTGAAAGGAGCTACAGTGTTCCCTAAGATGGA

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	32.30%	24.30%	0.74%	42.62%	NA
All Indica	2759	4.30%	33.10%	1.16%	61.44%	NA
All Japonica	1512	89.80%	8.40%	0.00%	1.79%	NA
Aus	269	1.90%	0.40%	1.12%	96.65%	NA
Indica I	595	5.40%	72.10%	0.34%	22.18%	NA
Indica II	465	4.10%	12.70%	1.08%	82.15%	NA
Indica III	913	1.40%	28.50%	1.20%	68.89%	NA
Indica Intermediate	786	7.10%	20.90%	1.78%	70.23%	NA
Temperate Japonica	767	97.90%	2.00%	0.00%	0.13%	NA
Tropical Japonica	504	89.90%	5.20%	0.00%	4.96%	NA
Japonica Intermediate	241	63.90%	35.70%	0.00%	0.41%	NA
VI/Aromatic	96	2.10%	92.70%	0.00%	5.21%	NA
Intermediate	90	46.70%	23.30%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321809345	A -> DEL	LOC_Os03g39250.1	N	frameshift_variant	Average:45.782; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0321809345	A -> G	LOC_Os03g39250.1	missense_variant&splice_region_variant ; p.Tyr592His; MODERATE	nonsynonymous_codon ; Y592H	Average:45.782; most accessible tissue: Minghui63 flag leaf, score: 73.752	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321809345	NA	1.14E-07	mr1074	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
vg0321809345	NA	2.65E-08	mr1081	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
vg0321809345	NA	1.10E-10	mr1130	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
vg0321809345	NA	9.37E-10	mr1148	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
vg0321809345	NA	9.83E-07	mr1245	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
vg0321809345	NA	1.08E-07	mr1254	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
vg0321809345	NA	4.67E-06	mr1857	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