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Detailed information for vg1110726582:

Variant ID: vg1110726582 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10726582
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTCTCAATAAGGGGTGAGAATACATGATGAGGATGTTAGGTCCCGATCTTCCGATAGGTATTGATAAACGGTCGATTTGGGCAGAGTCACGACACA[G/A]
CTCGATCTGGCTTCTGAACAAACACACTCTTGAGCCCCGCAATCGCAGCACCACGTCCCCTCTGGTTATCACCCGTGTCGAAACGCGGATGGCCTTGCCG

Reverse complement sequence

CGGCAAGGCCATCCGCGTTTCGACACGGGTGATAACCAGAGGGGACGTGGTGCTGCGATTGCGGGGCTCAAGAGTGTGTTTGTTCAGAAGCCAGATCGAG[C/T]
TGTGTCGTGACTCTGCCCAAATCGACCGTTTATCAATACCTATCGGAAGATCGGGACCTAACATCCTCATCATGTATTCTCACCCCTTATTGAGAAATTT

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	96.20%	2.70%	1.10%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	88.80%	8.20%	3.04%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	79.00%	15.90%	5.08%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	97.50%	0.80%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg1110726582	G -> A	LOC_Os11g18860-LOC_Os11g18870	intergenic_region ; MODIFIER	silent_mutation	Average:32.699; most accessible tissue: Zhenshan97 young leaf, score: 55.261	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110726582	3.35E-06	1.56E-06	mr1321_2	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