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Detailed information for vg1100495758:

Variant ID: vg1100495758 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 495758
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCGCCGCCGCGTCCAAGCCCGAGGGTGGCGACGAGAGGCTTGGCACCTCCGTCCCCGCCGCCCCGAGGCAGCGGATGATCACATGCGACGAGGTCCC[G/A]
GTCAAGGAAGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGGATCGGTGGTCTTCTGGACGACAAATAGGAAGACGCGCTCGTCTCCTTCCTGCGGG

Reverse complement sequence

CCCGCAGGAAGGAGACGAGCGCGTCTTCCTATTTGTCGTCCAGAAGACCACCGATCCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACTTCCTTGAC[C/T]
GGGACCTCGTCGCATGTGATCATCCGCTGCCTCGGGGCGGCGGGGACGGAGGTGCCAAGCCTCTCGTCGCCACCCTCGGGCTTGGACGCGGCGGCGAGGT

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	39.30%	39.10%	15.34%	6.20%	NA
All Indica	2759	62.10%	6.60%	22.58%	8.74%	NA
All Japonica	1512	2.50%	96.30%	1.12%	0.07%	NA
Aus	269	8.90%	48.30%	26.02%	16.73%	NA
Indica I	595	64.70%	1.20%	18.82%	15.29%	NA
Indica II	465	72.70%	13.10%	12.04%	2.15%	NA
Indica III	913	53.60%	5.00%	34.17%	7.23%	NA
Indica Intermediate	786	63.60%	8.80%	18.19%	9.41%	NA
Temperate Japonica	767	2.20%	96.60%	1.04%	0.13%	NA
Tropical Japonica	504	1.40%	98.00%	0.60%	0.00%	NA
Japonica Intermediate	241	5.80%	91.70%	2.49%	0.00%	NA
VI/Aromatic	96	59.40%	29.20%	6.25%	5.21%	NA
Intermediate	90	31.10%	57.80%	10.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100495758	G -> A	LOC_Os11g01920.1	splice_region_variant&synonymous_variant ; p.Pro785Pro; LOW	synonymous_codon	Average:65.469; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg1100495758	G -> DEL	LOC_Os11g01920.1	N	frameshift_variant	Average:65.469; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100495758	2.35E-06	2.35E-06	mr1770	Jap_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