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Detailed information for vg0315264922:

Variant ID: vg0315264922 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15264922
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGTTAGAACTCATCAAGGATTATGATGTGGGAATCCACTATCATCCTGGTAAGGCCAACGTGGTCGCCGACGCTCTTGGCGTCCGTGGCATTCCACCG[G/A]
AACTTAATCAACAGATGGAAGCCCTGAACCTAAGCATAGTTGGTCGTGGATTCTTGGCTACGCTGGAAGCCAAGCCTACCTTGCTCGATCAAATCCGCGA

Reverse complement sequence

TCGCGGATTTGATCGAGCAAGGTAGGCTTGGCTTCCAGCGTAGCCAAGAATCCACGACCAACTATGCTTAGGTTCAGGGCTTCCATCTGTTGATTAAGTT[C/T]
CGGTGGAATGCCACGGACGCCAAGAGCGTCGGCGACCACGTTGGCCTTACCAGGATGATAGTGGATTCCCACATCATAATCCTTGATGAGTTCTAACCAT

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	70.10%	12.00%	15.91%	1.90%	NA
All Indica	2759	60.10%	19.20%	20.66%	0.07%	NA
All Japonica	1512	85.00%	0.10%	9.06%	5.82%	NA
Aus	269	75.50%	12.30%	12.27%	0.00%	NA
Indica I	595	77.60%	15.30%	7.06%	0.00%	NA
Indica II	465	67.30%	4.10%	28.39%	0.22%	NA
Indica III	913	40.70%	33.80%	25.41%	0.00%	NA
Indica Intermediate	786	65.00%	14.00%	20.87%	0.13%	NA
Temperate Japonica	767	95.40%	0.10%	1.83%	2.61%	NA
Tropical Japonica	504	80.00%	0.00%	17.06%	2.98%	NA
Japonica Intermediate	241	62.20%	0.40%	15.35%	21.99%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	83.30%	5.60%	11.11%	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
vg0315264922	G -> A	LOC_Os03g26750.1	intron_variant ; MODIFIER	silent_mutation	Average:22.182; most accessible tissue: Zhenshan97 flag leaf, score: 35.167	N	N	N	N
vg0315264922	G -> DEL	N	N	silent_mutation	Average:22.182; most accessible tissue: Zhenshan97 flag leaf, score: 35.167	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315264922	NA	2.59E-09	mr1218_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
vg0315264922	NA	6.23E-06	mr1232_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
vg0315264922	NA	8.37E-06	mr1442_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
vg0315264922	1.31E-06	NA	mr1519_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
vg0315264922	6.73E-07	2.84E-12	mr1519_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
vg0315264922	NA	2.58E-06	mr1539_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