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Detailed information for vg0722036907:

Variant ID: vg0722036907 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22036907
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTGGGACGGAGGGAGTATTTATTCTCAAGTAGCTCAAGATTACCAAATTTAATCTATTCAGATTGTTATGTGCAAGCAGATCATAACACCTGAATTG[A/G]
AGCACATGTTGGGACTCTATCAAATGTTAACATGTGCAGTCAGGCCTCCTCATAGGTTAAACATAAAAATTCTAATACATGGTGGATGGCTCAATGTGTT

Reverse complement sequence

AACACATTGAGCCATCCACCATGTATTAGAATTTTTATGTTTAACCTATGAGGAGGCCTGACTGCACATGTTAACATTTGATAGAGTCCCAACATGTGCT[T/C]
CAATTCAGGTGTTATGATCTGCTTGCACATAACAATCTGAATAGATTAAATTTGGTAATCTTGAGCTACTTGAGAATAAATACTCCCTCCGTCCCAAAAT

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	94.30%	5.70%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	82.50%	17.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.60%	4.40%	0.00%	0.00%	NA
Tropical Japonica	504	67.70%	32.30%	0.00%	0.00%	NA
Japonica Intermediate	241	71.80%	28.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0722036907	A -> G	LOC_Os07g36770.1	upstream_gene_variant ; 2047.0bp to feature; MODIFIER	silent_mutation	Average:45.618; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0722036907	A -> G	LOC_Os07g36780.1	downstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:45.618; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0722036907	A -> G	LOC_Os07g36770-LOC_Os07g36780	intergenic_region ; MODIFIER	silent_mutation	Average:45.618; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722036907	4.79E-06	4.62E-15	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0722036907	NA	1.71E-06	Grain_weight	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0722036907	NA	1.90E-06	mr1156	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
vg0722036907	NA	6.37E-08	mr1179	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
vg0722036907	NA	7.67E-06	mr1188	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
vg0722036907	NA	2.37E-06	mr1213	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
vg0722036907	NA	4.00E-06	mr1224	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
vg0722036907	NA	5.16E-09	mr1563	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
vg0722036907	NA	9.39E-08	mr1668	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