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Detailed information for vg0403035005:

Variant ID: vg0403035005 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3035005
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, C: 0.15, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCCCTGTTTGTGCATTTGACAAAAAAAATTCTGGGTTGTGTGCCCCATCAAGATCTTATTATTCTCTTTCAAAATTGTCAATGTATCAGTAGACAAAC[C/A]
AGCAGATGTTTGGGTGTTCGTTTATAATCTAAATGCCTGTAATGCTTATTTTGGATTGTAACATTTTTTACAGCATGTATATTGTACATTAAATCTACTG

Reverse complement sequence

CAGTAGATTTAATGTACAATATACATGCTGTAAAAAATGTTACAATCCAAAATAAGCATTACAGGCATTTAGATTATAAACGAACACCCAAACATCTGCT[G/T]
GTTTGTCTACTGATACATTGACAATTTTGAAAGAGAATAATAAGATCTTGATGGGGCACACAACCCAGAATTTTTTTTGTCAAATGCACAAACAGGGCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.10%	19.00%	0.30%	37.60%	NA
All Indica	2759	62.30%	6.60%	0.25%	30.84%	NA
All Japonica	1512	13.90%	36.70%	0.26%	49.14%	NA
Aus	269	2.20%	53.90%	0.37%	43.49%	NA
Indica I	595	90.30%	7.90%	0.00%	1.85%	NA
Indica II	465	53.30%	11.80%	0.43%	34.41%	NA
Indica III	913	52.10%	1.40%	0.22%	46.22%	NA
Indica Intermediate	786	58.30%	8.50%	0.38%	32.82%	NA
Temperate Japonica	767	9.90%	63.10%	0.39%	26.60%	NA
Tropical Japonica	504	13.30%	5.20%	0.20%	81.35%	NA
Japonica Intermediate	241	27.80%	18.70%	0.00%	53.53%	NA
VI/Aromatic	96	55.20%	2.10%	1.04%	41.67%	NA
Intermediate	90	54.40%	15.60%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403035005	C -> DEL	N	N	silent_mutation	Average:8.339; most accessible tissue: Callus, score: 17.314	N	N	N	N
vg0403035005	C -> A	LOC_Os04g05880.1	intron_variant ; MODIFIER	silent_mutation	Average:8.339; most accessible tissue: Callus, score: 17.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403035005	NA	1.73E-06	mr1164	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
vg0403035005	NA	1.98E-06	mr1183	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
vg0403035005	NA	1.88E-06	mr1503	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
vg0403035005	NA	2.85E-07	mr1763	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
vg0403035005	NA	2.23E-07	mr1180_2	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