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Detailed information for vg0336089219:

Variant ID: vg0336089219 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 36089219
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ATCATAAAAGTCTTACATAAATGCAGCGGAAAAACGAAAGACAACAGGAGCTAAGCCTTGACTAGAACTGCAGCGGGAACACCACTCCACAGGCATCCTC[A/G]
ACGGCACGGACGAAGCCTACTCCTCGGAGAAACCTCCATCTGACACATACTCATACTCTGGGGTTGGGAAAAATAGAGCAAGACTGAGTACTACCCACTG

Reverse complement sequence

CAGTGGGTAGTACTCAGTCTTGCTCTATTTTTCCCAACCCCAGAGTATGAGTATGTGTCAGATGGAGGTTTCTCCGAGGAGTAGGCTTCGTCCGTGCCGT[T/C]
GAGGATGCCTGTGGAGTGGTGTTCCCGCTGCAGTTCTAGTCAAGGCTTAGCTCCTGTTGTCTTTCGTTTTTCCGCTGCATTTATGTAAGACTTTTATGAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.80%	10.20%	11.45%	9.52%	NA
All Indica	2759	52.70%	12.10%	19.17%	16.06%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.07%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	46.20%	4.00%	18.49%	31.26%	NA
Indica II	465	68.20%	11.40%	9.89%	10.54%	NA
Indica III	913	45.20%	17.30%	27.27%	10.19%	NA
Indica Intermediate	786	57.10%	12.50%	15.78%	14.63%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.20%	0.60%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	6.70%	10.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0336089219	A -> DEL	N	N	silent_mutation	Average:21.363; most accessible tissue: Zhenshan97 root, score: 60.612	N	N	N	N
vg0336089219	A -> G	LOC_Os03g63870.1	intron_variant ; MODIFIER	silent_mutation	Average:21.363; most accessible tissue: Zhenshan97 root, score: 60.612	N	N	N	N
vg0336089219	A -> G	LOC_Os03g63870.2	intron_variant ; MODIFIER	silent_mutation	Average:21.363; most accessible tissue: Zhenshan97 root, score: 60.612	N	N	N	N
vg0336089219	A -> G	LOC_Os03g63870.3	intron_variant ; MODIFIER	silent_mutation	Average:21.363; most accessible tissue: Zhenshan97 root, score: 60.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0336089219	NA	4.41E-06	mr1291	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
vg0336089219	2.92E-06	1.33E-07	mr1892	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
vg0336089219	4.18E-07	1.18E-07	mr1892	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
vg0336089219	NA	6.55E-06	mr1975	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