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Detailed information for vg1101177321:

Variant ID: vg1101177321 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1177321
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CAAACACCGCTGCTAACGCTCCAAAGGTGCCCGAAGGAAAAGATCCCTATGTTGTGAAGGAGTATCTCAAGGGAAAAGATTATAACATTTATGTGCACAG[G/A]
TCAATTAATAAGTTCATGCTCTTGTTAAGTATAATTTGATCTTTGTTTAATTTTATATCTTGATCCACTGCAAGCTGGTGAATAATATACTACTTAGAAA

Reverse complement sequence

TTTCTAAGTAGTATATTATTCACCAGCTTGCAGTGGATCAAGATATAAAATTAAACAAAGATCAAATTATACTTAACAAGAGCATGAACTTATTAATTGA[C/T]
CTGTGCACATAAATGTTATAATCTTTTCCCTTGAGATACTCCTTCACAACATAGGGATCTTTTCCTTCGGGCACCTTTGGAGCGTTAGCAGCGGTGTTTG

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	89.40%	8.00%	2.62%	0.00%	NA
All Indica	2759	82.40%	13.30%	4.31%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	91.80%	1.50%	6.72%	0.00%	NA
Indica II	465	75.70%	18.90%	5.38%	0.00%	NA
Indica III	913	75.90%	22.60%	1.53%	0.00%	NA
Indica Intermediate	786	86.80%	8.10%	5.09%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	2.22%	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
vg1101177321	G -> A	LOC_Os11g03230.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:46.94; most accessible tissue: Minghui63 flower, score: 64.685	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101177321	NA	1.41E-08	mr1718	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
vg1101177321	4.93E-06	NA	mr1750	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
vg1101177321	1.29E-06	9.47E-10	mr1750	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
vg1101177321	NA	8.12E-06	mr1842	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