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Detailed information for vg1115987263:

Variant ID: vg1115987263 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15987263
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAGCGACATTCTTGATAGCCAATTTCAGCCTTGCCTTCTGTTCTTCGACAGCTTGTGGGAGATCGGCTAGCTTCTTGTGCTCCATATCCAGCTCGGC[A/G]
TTGCATTCTTGAAGTTGTGCCATGAGATCAATCTTACGAACTTCAAGCCGATCAATATTGGACTTGATCGGGCCCTCAGACAGCTGATCAAGCTTAGACT

Reverse complement sequence

AGTCTAAGCTTGATCAGCTGTCTGAGGGCCCGATCAAGTCCAATATTGATCGGCTTGAAGTTCGTAAGATTGATCTCATGGCACAACTTCAAGAATGCAA[T/C]
GCCGAGCTGGATATGGAGCACAAGAAGCTAGCCGATCTCCCACAAGCTGTCGAAGAACAGAAGGCAAGGCTGAAATTGGCTATCAAGAATGTCGCTGATA

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	39.90%	15.90%	9.25%	34.93%	NA
All Indica	2759	9.90%	24.90%	12.79%	52.41%	NA
All Japonica	1512	96.10%	0.30%	0.46%	3.11%	NA
Aus	269	13.00%	19.30%	23.05%	44.61%	NA
Indica I	595	13.10%	15.60%	11.43%	59.83%	NA
Indica II	465	4.30%	32.90%	12.04%	50.75%	NA
Indica III	913	8.80%	29.20%	13.36%	48.63%	NA
Indica Intermediate	786	12.20%	22.00%	13.61%	52.16%	NA
Temperate Japonica	767	95.30%	0.10%	0.52%	4.04%	NA
Tropical Japonica	504	96.80%	0.60%	0.40%	2.18%	NA
Japonica Intermediate	241	97.10%	0.40%	0.41%	2.07%	NA
VI/Aromatic	96	84.40%	3.10%	10.42%	2.08%	NA
Intermediate	90	47.80%	6.70%	5.56%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1115987263	A -> DEL	LOC_Os11g27770.1	N	frameshift_variant	Average:13.886; most accessible tissue: Callus, score: 34.303	N	N	N	N
vg1115987263	A -> G	LOC_Os11g27770.1	synonymous_variant ; p.Asn288Asn; LOW	synonymous_codon	Average:13.886; most accessible tissue: Callus, score: 34.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115987263	2.86E-06	7.24E-07	mr1426	Ind_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