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Detailed information for vg0332500781:

Variant ID: vg0332500781 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32500781
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGCAAAAAAGCATGTTCTATCACCACAATTTTAATTTTTGTGGCAATTTATATAGTACATGGTACTTTTCACTATTTTTTGTTGCCACGATCAACAA[A/G]
TTCGTTGCAATAAAAAAATTGTTGTCTCATAATTTAACTTATTTTTTTCATATGGACTCGGATTGAGACAAATTTTATATGGAAATTATAGCTCTCGACG

Reverse complement sequence

CGTCGAGAGCTATAATTTCCATATAAAATTTGTCTCAATCCGAGTCCATATGAAAAAAATAAGTTAAATTATGAGACAACAATTTTTTTATTGCAACGAA[T/C]
TTGTTGATCGTGGCAACAAAAAATAGTGAAAAGTACCATGTACTATATAAATTGCCACAAAAATTAAAATTGTGGTGATAGAACATGCTTTTTTGCAATA

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	92.00%	2.00%	3.34%	2.67%	NA
All Indica	2759	86.70%	3.20%	5.55%	4.49%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.80%	1.80%	5.88%	1.51%	NA
Indica II	465	88.80%	3.20%	3.01%	4.95%	NA
Indica III	913	86.30%	2.80%	3.50%	7.34%	NA
Indica Intermediate	786	83.00%	4.70%	9.16%	3.18%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	3.30%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0332500781	A -> DEL	N	N	silent_mutation	Average:20.162; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0332500781	A -> G	LOC_Os03g57020-LOC_Os03g57030	intergenic_region ; MODIFIER	silent_mutation	Average:20.162; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332500781	6.82E-07	NA	mr1723	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
vg0332500781	3.55E-07	8.90E-09	mr1723	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
vg0332500781	NA	8.05E-06	mr1734	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
vg0332500781	5.57E-09	NA	mr1723_2	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
vg0332500781	8.73E-09	5.50E-13	mr1723_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