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Detailed information for vg1126345088:

Variant ID: vg1126345088 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26345088
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGACCGAGACCGAAAATACCAAGGCTGAGAAATTCGGTCTCAGTCATCAAAAACCGAATTTTTTTCGGCAATTCGGTTATTGGCTTCGGTTAATTGA[G/A]
TTACCCGAGAAAACCGAATTGTGGCCCAATAGGCCTATGAGGGCAACAGGGAGGGATTAAGTCACGCCGCGCCGCCTCCAATCCAATCCCCGCCGCATCG

Reverse complement sequence

CGATGCGGCGGGGATTGGATTGGAGGCGGCGCGGCGTGACTTAATCCCTCCCTGTTGCCCTCATAGGCCTATTGGGCCACAATTCGGTTTTCTCGGGTAA[C/T]
TCAATTAACCGAAGCCAATAACCGAATTGCCGAAAAAAATTCGGTTTTTGATGACTGAGACCGAATTTCTCAGCCTTGGTATTTTCGGTCTCGGTCTCGG

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	73.40%	25.90%	0.32%	0.30%	NA
All Indica	2759	87.20%	12.00%	0.33%	0.43%	NA
All Japonica	1512	48.70%	51.00%	0.13%	0.13%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	90.30%	9.60%	0.17%	0.00%	NA
Indica II	465	89.20%	10.80%	0.00%	0.00%	NA
Indica III	913	90.00%	8.70%	0.44%	0.88%	NA
Indica Intermediate	786	80.50%	18.40%	0.51%	0.51%	NA
Temperate Japonica	767	22.30%	77.60%	0.13%	0.00%	NA
Tropical Japonica	504	83.90%	15.50%	0.20%	0.40%	NA
Japonica Intermediate	241	59.30%	40.70%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	92.70%	2.08%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg1126345088	G -> A	LOC_Os11g43650-LOC_Os11g43660	intergenic_region ; MODIFIER	silent_mutation	Average:54.061; most accessible tissue: Zhenshan97 young leaf, score: 76.773	N	N	N	N
vg1126345088	G -> DEL	N	N	silent_mutation	Average:54.061; most accessible tissue: Zhenshan97 young leaf, score: 76.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126345088	NA	7.80E-08	mr1252	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
vg1126345088	6.08E-06	6.08E-06	mr1462	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
vg1126345088	NA	5.59E-08	mr1829	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
vg1126345088	NA	3.53E-07	mr1977	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
vg1126345088	NA	1.08E-06	mr1133_2	Ind_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
vg1126345088	NA	1.64E-06	mr1582_2	Ind_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
vg1126345088	NA	3.22E-06	mr1715_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
vg1126345088	NA	9.96E-09	mr1829_2	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