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Detailed information for vg0308084937:

Variant ID: vg0308084937 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8084937
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGACGAGCCCACGAGTCAGTGACTCGGTGCACGGGAGAGAGGGTTTACGCGGCGCGGGGGAGCTAGTGTTTGCGGACGCGGCTCACAGATGGTGCACC[A/G]
GGTGGACTGGGAGACGGCGGGCCCAAGCGCAGCCGGCTGGCTCTCCGTGGACCACGCGCGTACAGGAGAACGGATCGGAGGAGCGGTTGACTGAGGTCAA

Reverse complement sequence

TTGACCTCAGTCAACCGCTCCTCCGATCCGTTCTCCTGTACGCGCGTGGTCCACGGAGAGCCAGCCGGCTGCGCTTGGGCCCGCCGTCTCCCAGTCCACC[T/C]
GGTGCACCATCTGTGAGCCGCGTCCGCAAACACTAGCTCCCCCGCGCCGCGTAAACCCTCTCTCCCGTGCACCGAGTCACTGACTCGTGGGCTCGTCCCA

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	89.20%	10.00%	0.80%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	67.30%	30.20%	2.51%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	41.70%	54.50%	3.78%	0.00%	NA
Tropical Japonica	504	96.00%	2.60%	1.39%	0.00%	NA
Japonica Intermediate	241	88.80%	10.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0308084937	A -> G	LOC_Os03g14840.1	upstream_gene_variant ; 2224.0bp to feature; MODIFIER	silent_mutation	Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0308084937	A -> G	LOC_Os03g14820-LOC_Os03g14840	intergenic_region ; MODIFIER	silent_mutation	Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308084937	NA	1.44E-12	Heading_date	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
vg0308084937	NA	3.39E-10	Heading_date	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
vg0308084937	NA	4.09E-14	Spikelet_length	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
vg0308084937	NA	4.75E-09	mr1002_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
vg0308084937	NA	3.59E-06	mr1330_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
vg0308084937	NA	5.83E-06	mr1354_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
vg0308084937	NA	3.06E-06	mr1647_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
vg0308084937	2.90E-06	1.32E-07	mr1648_2	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
vg0308084937	NA	4.07E-06	mr1851_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