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Detailed information for vg1108548494:

Variant ID: vg1108548494 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8548494
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGAAGAATACACGACCTCTACCACTTGTTGCTATCCTGGAGGGCATCACGAGGGGTACACAGAAGTATCTCTGTAAAAGGTATTCCATGGCTAGTCT[G/T]
AACCTTAGCAAACCCAGTGTTAAGTATAGCCCCGCTATTACACAGTACATGGATGAGAAAAGTAAGAAGGGAGGAATCCACAGAGTGTGGCCTGCTGGGA

Reverse complement sequence

TCCCAGCAGGCCACACTCTGTGGATTCCTCCCTTCTTACTTTTCTCATCCATGTACTGTGTAATAGCGGGGCTATACTTAACACTGGGTTTGCTAAGGTT[C/A]
AGACTAGCCATGGAATACCTTTTACAGAGATACTTCTGTGTACCCCTCGTGATGCCCTCCAGGATAGCAACAAGTGGTAGAGGTCGTGTATTCTTCATAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	21.00%	0.30%	5.29%	73.42%	NA
All Indica	2759	2.80%	0.40%	2.90%	93.95%	NA
All Japonica	1512	45.30%	0.10%	8.86%	45.70%	NA
Aus	269	72.50%	0.00%	0.37%	27.14%	NA
Indica I	595	3.40%	0.30%	2.35%	93.95%	NA
Indica II	465	1.70%	0.00%	1.51%	96.77%	NA
Indica III	913	0.90%	0.30%	3.40%	95.40%	NA
Indica Intermediate	786	5.10%	0.80%	3.56%	90.59%	NA
Temperate Japonica	767	73.00%	0.00%	3.91%	23.08%	NA
Tropical Japonica	504	8.50%	0.00%	16.27%	75.20%	NA
Japonica Intermediate	241	34.00%	0.80%	9.13%	56.02%	NA
VI/Aromatic	96	19.80%	0.00%	26.04%	54.17%	NA
Intermediate	90	20.00%	0.00%	11.11%	68.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108548494	G -> T	LOC_Os11g15170.1	synonymous_variant ; p.Leu767Leu; LOW	synonymous_codon	Average:18.969; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1108548494	G -> DEL	LOC_Os11g15170.1	N	frameshift_variant	Average:18.969; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108548494	NA	2.56E-07	mr1083	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
vg1108548494	NA	2.35E-06	mr1408	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
vg1108548494	1.03E-06	1.99E-08	mr1653	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
vg1108548494	NA	9.58E-06	mr1860	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