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Detailed information for vg0225214833:

Variant ID: vg0225214833 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25214833
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTAAGGATGGTAAAATTATCTTATTAATTAATATAAGACTATTTTTTAATGTACTAAGTGAAATACATATTTTTTTTTTGAAACTAGAAAAATATCC[G/A]
TGCGTTGCAATCGGTGAAGTCTATTTTAATCTTATTATTGTTATATGCTTTAGTTCAGATGAAATTCACTATGTGAGTTCGGTTGGATATATATATTTTT

Reverse complement sequence

AAAAATATATATATCCAACCGAACTCACATAGTGAATTTCATCTGAACTAAAGCATATAACAATAATAAGATTAAAATAGACTTCACCGATTGCAACGCA[C/T]
GGATATTTTTCTAGTTTCAAAAAAAAAATATGTATTTCACTTAGTACATTAAAAAATAGTCTTATATTAATTAATAAGATAATTTTACCATCCTTAAAAA

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	73.20%	26.50%	0.30%	0.04%	NA
All Indica	2759	82.40%	17.20%	0.40%	0.04%	NA
All Japonica	1512	51.30%	48.60%	0.07%	0.07%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	77.30%	21.80%	0.84%	0.00%	NA
Indica II	465	76.80%	23.00%	0.22%	0.00%	NA
Indica III	913	91.90%	8.00%	0.00%	0.11%	NA
Indica Intermediate	786	78.50%	20.90%	0.64%	0.00%	NA
Temperate Japonica	767	58.80%	41.10%	0.00%	0.13%	NA
Tropical Japonica	504	45.20%	54.60%	0.20%	0.00%	NA
Japonica Intermediate	241	39.80%	60.20%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	74.40%	23.30%	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
vg0225214833	G -> A	LOC_Os02g41961.1	intron_variant ; MODIFIER	silent_mutation	Average:22.631; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0225214833	G -> DEL	N	N	silent_mutation	Average:22.631; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225214833	1.60E-06	1.60E-06	mr1571	Jap_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
vg0225214833	NA	7.32E-06	mr1707	Jap_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
vg0225214833	NA	7.16E-06	mr1233_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
vg0225214833	NA	5.01E-06	mr1457_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