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Detailed information for vg1112624940:

Variant ID: vg1112624940 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12624940
Reference Allele: A	Alternative Allele: G
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: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CCACACACCGGTATAACCATGCCCCACACGACTCTAGCAGGAAAACAAACGAAAAGAACACACGCGCGAGCCTACTAACTGCTCGTCTACTTCTGCGACG[A/G]
GCCAGGGCGGAAGGTGAGCAGCAGCGCATCCTCCGTGCTGCCAACGCCAGAGGCTCCCTCCTCCTGAGGAACCGAGGGTGCGGGCTCGGCGCGAGGGGTC

Reverse complement sequence

GACCCCTCGCGCCGAGCCCGCACCCTCGGTTCCTCAGGAGGAGGGAGCCTCTGGCGTTGGCAGCACGGAGGATGCGCTGCTGCTCACCTTCCGCCCTGGC[T/C]
CGTCGCAGAAGTAGACGAGCAGTTAGTAGGCTCGCGCGTGTGTTCTTTTCGTTTGTTTTCCTGCTAGAGTCGTGTGGGGCATGGTTATACCGGTGTGTGG

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	66.00%	33.90%	0.15%	0.00%	NA
All Indica	2759	98.00%	1.90%	0.04%	0.00%	NA
All Japonica	1512	5.10%	94.70%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.60%	0.13%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	8.30%	91.10%	0.60%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	60.00%	36.70%	3.33%	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
vg1112624940	A -> G	LOC_Os11g21980.1	intron_variant ; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Zhenshan97 flag leaf, score: 79.935	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112624940	NA	4.63E-09	mr1336	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
vg1112624940	NA	1.02E-89	mr1758	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
vg1112624940	2.85E-06	2.85E-06	mr1758	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