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Detailed information for vg0503608486:

Variant ID: vg0503608486 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3608486
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.06, others allele: 0.00, population size: 163. )

Flanking Sequence (100 bp) in Reference Genome:

GACATTATTATCATAGCTAAACTGGCATTGATGAGTTAGTAGTTTCCATTACCAGAGTAAAAAAATGACATTCCTAATGACTAGGACTTGTTCTTTTTTT[A/T]
AAAAAAAAAGATAATAATGTCGGTTGTGCAGCTGTGTGCGACTATGGAGGAGGAGTGGGGAATGTGGGGAGCTGCGGGCTTGGTGCCAGGAGGAAGCTTG

Reverse complement sequence

CAAGCTTCCTCCTGGCACCAAGCCCGCAGCTCCCCACATTCCCCACTCCTCCTCCATAGTCGCACACAGCTGCACAACCGACATTATTATCTTTTTTTTT[T/A]
AAAAAAAGAACAAGTCCTAGTCATTAGGAATGTCATTTTTTTACTCTGGTAATGGAAACTACTAACTCATCAATGCCAGTTTAGCTATGATAATAATGTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.30%	34.60%	9.65%	7.38%	NA
All Indica	2759	37.70%	34.30%	15.55%	12.54%	NA
All Japonica	1512	76.30%	22.80%	0.99%	0.00%	NA
Aus	269	5.60%	92.20%	2.23%	0.00%	NA
Indica I	595	59.30%	6.40%	30.59%	3.70%	NA
Indica II	465	29.90%	44.90%	16.77%	8.39%	NA
Indica III	913	30.40%	41.70%	4.05%	23.77%	NA
Indica Intermediate	786	34.20%	40.30%	16.79%	8.65%	NA
Temperate Japonica	767	75.00%	24.10%	0.91%	0.00%	NA
Tropical Japonica	504	81.20%	18.30%	0.60%	0.00%	NA
Japonica Intermediate	241	70.10%	27.80%	2.07%	0.00%	NA
VI/Aromatic	96	26.00%	72.90%	1.04%	0.00%	NA
Intermediate	90	57.80%	33.30%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0503608486	A -> T	LOC_Os05g06880.1	downstream_gene_variant ; 4798.0bp to feature; MODIFIER	silent_mutation	Average:71.545; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0503608486	A -> T	LOC_Os05g06900.1	downstream_gene_variant ; 3663.0bp to feature; MODIFIER	silent_mutation	Average:71.545; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0503608486	A -> T	LOC_Os05g06890.1	intron_variant ; MODIFIER	silent_mutation	Average:71.545; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0503608486	A -> DEL	N	N	silent_mutation	Average:71.545; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503608486	NA	1.36E-06	mr1113_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
vg0503608486	NA	3.13E-06	mr1114_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
vg0503608486	NA	4.83E-06	mr1117_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
vg0503608486	NA	1.17E-06	mr1119_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
vg0503608486	2.12E-06	1.50E-07	mr1120_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
vg0503608486	NA	5.73E-07	mr1247_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