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Detailed information for vg0225214584:

Variant ID: vg0225214584 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25214584
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

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

Flanking Sequence (100 bp) in Reference Genome:

TAGGTGTCTTGTTTGGACTGGACGTATAATTAAATTACTATATTTGATATATATAGATTCATCTAATAAAGTAATATATCTTCATAATAATATTACTCAA[T/C]
TGATGTTTACATATTAACTAGAAAAATTGTACTGTACTTAAGAAAGTACTTGGGTACCAATATTTTACACTAAAAAATTAGTATCTCGAGATATCAAGTA

Reverse complement sequence

TACTTGATATCTCGAGATACTAATTTTTTAGTGTAAAATATTGGTACCCAAGTACTTTCTTAAGTACAGTACAATTTTTCTAGTTAATATGTAAACATCA[A/G]
TTGAGTAATATTATTATGAAGATATATTACTTTATTAGATGAATCTATATATATCAAATATAGTAATTTAATTATACGTCCAGTCCAAACAAGACACCTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.60%	36.30%	0.08%	0.00%	NA
All Indica	2759	46.00%	53.90%	0.11%	0.00%	NA
All Japonica	1512	94.50%	5.40%	0.07%	0.00%	NA
Aus	269	74.00%	26.00%	0.00%	0.00%	NA
Indica I	595	29.70%	70.10%	0.17%	0.00%	NA
Indica II	465	50.30%	49.70%	0.00%	0.00%	NA
Indica III	913	51.50%	48.40%	0.11%	0.00%	NA
Indica Intermediate	786	49.20%	50.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	86.50%	13.30%	0.20%	0.00%	NA
Japonica Intermediate	241	95.00%	5.00%	0.00%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg0225214584	T -> C	LOC_Os02g41961.1	intron_variant ; MODIFIER	silent_mutation	Average:46.136; most accessible tissue: Minghui63 flower, score: 66.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225214584	NA	2.93E-06	mr1042_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
vg0225214584	NA	4.29E-06	mr1291_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
vg0225214584	2.03E-06	2.56E-10	mr1457_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
vg0225214584	NA	2.19E-07	mr1458_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
vg0225214584	NA	5.42E-08	mr1690_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
vg0225214584	NA	6.73E-06	mr1892_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