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Detailed information for vg0231328780:

Variant ID: vg0231328780 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 31328780
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: 123. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTCAGAAGGTAGATTGGTTGCGCCGTTAGCACAGATTTGACGAGCGTAGTTCTTCCAGCCGCTGCCATGTTTTTTCCTCTCCAGCTTGCTACCCTTCC[G/A]
GAAATTTTGTTAAAGACAGGTTGCAAGTCCACCTTCCGCAGTCTTCCCAGAGCTAGGGGGAGGCCCAAGTACTTGATGGGGAAACTTGCCCTCACCACAG

Reverse complement sequence

CTGTGGTGAGGGCAAGTTTCCCCATCAAGTACTTGGGCCTCCCCCTAGCTCTGGGAAGACTGCGGAAGGTGGACTTGCAACCTGTCTTTAACAAAATTTC[C/T]
GGAAGGGTAGCAAGCTGGAGAGGAAAAAACATGGCAGCGGCTGGAAGAACTACGCTCGTCAAATCTGTGCTAACGGCGCAACCAATCTACCTTCTGACCG

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	88.00%	1.90%	10.11%	0.00%	NA
All Indica	2759	80.00%	3.10%	16.89%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	63.20%	4.40%	32.44%	0.00%	NA
Indica II	465	79.10%	7.30%	13.55%	0.00%	NA
Indica III	913	88.30%	0.00%	11.72%	0.00%	NA
Indica Intermediate	786	83.60%	3.30%	13.10%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	1.10%	7.78%	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
vg0231328780	G -> A	LOC_Os02g51200.1	synonymous_variant ; p.Ser1532Ser; LOW	synonymous_codon	Average:20.58; most accessible tissue: Callus, score: 35.205	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0231328780	8.71E-07	NA	mr1089	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
vg0231328780	4.74E-07	2.44E-06	mr1089	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