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Detailed information for vg1122062891:

Variant ID: vg1122062891 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22062891
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGCGGTCATGTGCAGCGTGGACAGGGACACGGCGAAGGCACCACGCTGCGCGGCCAGGAGCTCCCGCTGCGTCGCTCTCCTCCTCAACGGTGGCCACG[G/A]
GGCCAACAGCTGACGGTGGCCATGGGCGGGGAGATGTCGGTGGCGGCATCGGCGGTTAGGGCCTCCCGTATGGCTGGCTCGACTTCTTTCTTCTCGGACG

Reverse complement sequence

CGTCCGAGAAGAAAGAAGTCGAGCCAGCCATACGGGAGGCCCTAACCGCCGATGCCGCCACCGACATCTCCCCGCCCATGGCCACCGTCAGCTGTTGGCC[C/T]
CGTGGCCACCGTTGAGGAGGAGAGCGACGCAGCGGGAGCTCCTGGCCGCGCAGCGTGGTGCCTTCGCCGTGTCCCTGTCCACGCTGCACATGACCGCTGG

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	48.50%	45.90%	0.42%	5.21%	NA
All Indica	2759	28.50%	66.70%	0.54%	4.31%	NA
All Japonica	1512	83.50%	13.90%	0.26%	2.31%	NA
Aus	269	72.50%	2.60%	0.00%	24.91%	NA
Indica I	595	27.40%	72.10%	0.17%	0.34%	NA
Indica II	465	33.30%	64.10%	0.86%	1.72%	NA
Indica III	913	22.50%	69.10%	0.44%	8.00%	NA
Indica Intermediate	786	33.30%	61.30%	0.76%	4.58%	NA
Temperate Japonica	767	93.10%	6.10%	0.26%	0.52%	NA
Tropical Japonica	504	68.50%	26.40%	0.40%	4.76%	NA
Japonica Intermediate	241	84.60%	12.40%	0.00%	2.90%	NA
VI/Aromatic	96	11.50%	66.70%	1.04%	20.83%	NA
Intermediate	90	42.20%	52.20%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122062891	G -> A	LOC_Os11g37380.1	downstream_gene_variant ; 938.0bp to feature; MODIFIER	silent_mutation	Average:71.157; most accessible tissue: Zhenshan97 young leaf, score: 87.153	N	N	N	N
vg1122062891	G -> A	LOC_Os11g37380-LOC_Os11g37390	intergenic_region ; MODIFIER	silent_mutation	Average:71.157; most accessible tissue: Zhenshan97 young leaf, score: 87.153	N	N	N	N
vg1122062891	G -> DEL	N	N	silent_mutation	Average:71.157; most accessible tissue: Zhenshan97 young leaf, score: 87.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122062891	5.52E-06	8.40E-08	mr1698	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
vg1122062891	2.62E-06	2.02E-07	mr1517_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