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Detailed information for vg0314910245:

Variant ID: vg0314910245 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14910245
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

CATGATGAGTTTTGAAAGCGGTTTTAAACTCATCCTGTTCCACCATACGGATTTGATGATAACCGGCTCTCAAGTCCAGTTTAGAGAAGTATTGTGTGCC[C/T]
GCTAACTCATCCAATAACTCATCAACCACTGGCATTGGAAACTTACTCTTAACAGTGACAGAGTTGAGTTTGCGATAATCCACACAAAAACGCCATGTCC

Reverse complement sequence

GGACATGGCGTTTTTGTGTGGATTATCGCAAACTCAACTCTGTCACTGTTAAGAGTAAGTTTCCAATGCCAGTGGTTGATGAGTTATTGGATGAGTTAGC[G/A]
GGCACACAATACTTCTCTAAACTGGACTTGAGAGCCGGTTATCATCAAATCCGTATGGTGGAACAGGATGAGTTTAAAACCGCTTTCAAAACTCATCATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.70%	20.20%	0.06%	0.00%	NA
All Indica	2759	69.30%	30.60%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	67.30%	32.70%	0.00%	0.00%	NA
Indica I	595	42.40%	57.50%	0.17%	0.00%	NA
Indica II	465	57.80%	42.20%	0.00%	0.00%	NA
Indica III	913	89.50%	10.50%	0.00%	0.00%	NA
Indica Intermediate	786	73.00%	26.70%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0314910245	C -> T	LOC_Os03g26020.1	synonymous_variant ; p.Ala625Ala; LOW	synonymous_codon	Average:31.678; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314910245	NA	3.52E-06	mr1376	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
vg0314910245	NA	3.52E-06	mr1431	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
vg0314910245	NA	6.60E-07	mr1484	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
vg0314910245	3.66E-06	9.11E-07	mr1500	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
vg0314910245	6.25E-07	7.01E-08	mr1500	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
vg0314910245	4.95E-06	3.05E-07	mr1505	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
vg0314910245	9.74E-09	NA	mr1542	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
vg0314910245	4.89E-07	6.05E-07	mr1542	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
vg0314910245	NA	6.97E-06	mr1634	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
vg0314910245	4.62E-06	4.62E-06	mr1954	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
vg0314910245	NA	2.16E-07	mr1959	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
vg0314910245	4.43E-08	NA	mr1542_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
vg0314910245	1.13E-07	1.09E-07	mr1542_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
vg0314910245	NA	7.73E-06	mr1671_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