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Detailed information for vg0817029761:

Variant ID: vg0817029761 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17029761
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAGAAGAAGCTCGGAGGGCGGAGGAAGAAAACCGCAAAGAATATAATCCTCAACCAAAACCATGCGGCCCAGGATAGGTTCGGGTTCAATACCTCCT[G/A]
GTTCTCTCTCCATGGTCCCGCGACCAGGGAGGGCACCGTCATCCTGCAGCTTCTTCAGGGACGCGTTGGTGGAGGTGGACTTGTCGAGATCCATCGCCGC

Reverse complement sequence

GCGGCGATGGATCTCGACAAGTCCACCTCCACCAACGCGTCCCTGAAGAAGCTGCAGGATGACGGTGCCCTCCCTGGTCGCGGGACCATGGAGAGAGAAC[C/T]
AGGAGGTATTGAACCCGAACCTATCCTGGGCCGCATGGTTTTGGTTGAGGATTATATTCTTTGCGGTTTTCTTCCTCCGCCCTCCGAGCTTCTTCTTCTT

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	83.50%	16.00%	0.47%	0.00%	NA
All Indica	2759	98.90%	1.00%	0.04%	0.00%	NA
All Japonica	1512	59.90%	39.60%	0.46%	0.00%	NA
Aus	269	86.20%	8.60%	5.20%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	71.60%	27.80%	0.65%	0.00%	NA
Tropical Japonica	504	50.60%	49.20%	0.20%	0.00%	NA
Japonica Intermediate	241	42.30%	57.30%	0.41%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	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
vg0817029761	G -> A	LOC_Os08g27940.1	missense_variant ; p.Pro32Leu; MODERATE	nonsynonymous_codon ; P32L	Average:61.64; most accessible tissue: Zhenshan97 young leaf, score: 77.736	unknown	unknown	TOLERATED	0.17

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817029761	2.88E-06	NA	mr1006	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
vg0817029761	1.51E-06	NA	mr1007	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
vg0817029761	3.50E-06	NA	mr1052	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
vg0817029761	1.25E-06	NA	mr1410	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
vg0817029761	NA	3.24E-07	mr1057_2	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
vg0817029761	8.98E-06	NA	mr1410_2	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