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Detailed information for vg1118303285:

Variant ID: vg1118303285 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18303285
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

ACACTTCATCCGTCTCTCTTTATTGTAGATGCCATCTATACCACGGTTGCACCTTAATAGACTATATGCGAACTGTTTTGCAGAAAAACAATGGCAGTCC[G/A]
TCTGCTGCCCATACTCATGCCCCTCTGGTGGAAACCATGGTCGAACCTGATAATTCTTGGATGATATGTCGCATTTACAAGAAGAGGCAGCGTGCACCGC

Reverse complement sequence

GCGGTGCACGCTGCCTCTTCTTGTAAATGCGACATATCATCCAAGAATTATCAGGTTCGACCATGGTTTCCACCAGAGGGGCATGAGTATGGGCAGCAGA[C/T]
GGACTGCCATTGTTTTTCTGCAAAACAGTTCGCATATAGTCTATTAAGGTGCAACCGTGGTATAGATGGCATCTACAATAAAGAGAGACGGATGAAGTGT

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	89.60%	10.40%	0.02%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	69.90%	30.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	94.70%	5.30%	0.00%	0.00%	NA
Tropical Japonica	504	32.90%	67.10%	0.00%	0.00%	NA
Japonica Intermediate	241	68.50%	31.50%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1118303285	G -> A	LOC_Os11g31360.1	synonymous_variant ; p.Pro185Pro; LOW	synonymous_codon	Average:41.607; most accessible tissue: Callus, score: 66.833	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118303285	NA	4.94E-06	mr1192	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
vg1118303285	2.74E-07	3.06E-17	mr1871	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
vg1118303285	NA	4.48E-07	mr1871	Jap_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
vg1118303285	NA	5.12E-06	mr1194_2	Jap_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