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Detailed information for vg0318735765:

Variant ID: vg0318735765 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18735765
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.05, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

AACTCGAACAAATCGAGGAGGAGGATTTGGCTTTGGTTTCTTATTTGAAAAATTCTTTGCTAAGATTTTCTGATGGTAAAAAGAACCTCAACATGATTTT[G/A]
GATCAATCAGAGATTAGCACACATAACCGTGGTTTAGGTTTTAATCCTTATGCTCACAATTTTAGACATCCTCCTGTTGTGTTAGGTGTTGGTGCTAGAA

Reverse complement sequence

TTCTAGCACCAACACCTAACACAACAGGAGGATGTCTAAAATTGTGAGCATAAGGATTAAAACCTAAACCACGGTTATGTGTGCTAATCTCTGATTGATC[C/T]
AAAATCATGTTGAGGTTCTTTTTACCATCAGAAAATCTTAGCAAAGAATTTTTCAAATAAGAAACCAAAGCCAAATCCTCCTCCTCGATTTGTTCGAGTT

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	36.30%	0.20%	20.84%	42.72%	NA
All Indica	2759	5.00%	0.30%	25.08%	69.66%	NA
All Japonica	1512	90.30%	0.00%	8.93%	0.73%	NA
Aus	269	29.00%	0.00%	52.79%	18.22%	NA
Indica I	595	5.90%	0.80%	23.19%	70.08%	NA
Indica II	465	4.50%	0.20%	23.66%	71.61%	NA
Indica III	913	3.10%	0.10%	30.23%	66.59%	NA
Indica Intermediate	786	6.70%	0.10%	21.37%	71.76%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	75.00%	0.00%	23.41%	1.59%	NA
Japonica Intermediate	241	92.50%	0.00%	7.05%	0.41%	NA
VI/Aromatic	96	89.60%	0.00%	6.25%	4.17%	NA
Intermediate	90	52.20%	0.00%	11.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318735765	G -> A	LOC_Os03g32700.1	synonymous_variant ; p.Leu244Leu; LOW	synonymous_codon	Average:15.43; most accessible tissue: Callus, score: 39.922	N	N	N	N
vg0318735765	G -> DEL	LOC_Os03g32700.1	N	frameshift_variant	Average:15.43; most accessible tissue: Callus, score: 39.922	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318735765	6.16E-06	NA	mr1137	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
vg0318735765	3.47E-06	3.47E-06	mr1710	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