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Detailed information for vg0516242828:

Variant ID: vg0516242828 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16242828
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGAACAGTTTCAGAGCTTCAAGGGAGATCTGTACCAGAAATATATCCTGAAGGGGCAGACACCGAACTTCAACACATTACCAAAGCTAAGGGATCACT[G/A]
GGATGAGTTCGTTGCATATAAGACAGGTGAACAAGGGCAGGCGATGATGGAAAGAAACAAAGAAAATGCCGCCAAGAAGAAGTACCATCACCACTTGGGG

Reverse complement sequence

CCCCAAGTGGTGATGGTACTTCTTCTTGGCGGCATTTTCTTTGTTTCTTTCCATCATCGCCTGCCCTTGTTCACCTGTCTTATATGCAACGAACTCATCC[C/T]
AGTGATCCCTTAGCTTTGGTAATGTGTTGAAGTTCGGTGTCTGCCCCTTCAGGATATATTTCTGGTACAGATCTCCCTTGAAGCTCTGAAACTGTTCTGC

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	59.80%	40.00%	0.19%	0.00%	NA
All Indica	2759	84.80%	14.90%	0.25%	0.00%	NA
All Japonica	1512	24.10%	75.90%	0.00%	0.00%	NA
Aus	269	31.60%	68.40%	0.00%	0.00%	NA
Indica I	595	96.00%	4.00%	0.00%	0.00%	NA
Indica II	465	71.80%	28.20%	0.00%	0.00%	NA
Indica III	913	83.50%	16.40%	0.11%	0.00%	NA
Indica Intermediate	786	85.80%	13.50%	0.76%	0.00%	NA
Temperate Japonica	767	7.00%	93.00%	0.00%	0.00%	NA
Tropical Japonica	504	52.40%	47.60%	0.00%	0.00%	NA
Japonica Intermediate	241	19.50%	80.50%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	99.00%	1.04%	0.00%	NA
Intermediate	90	41.10%	57.80%	1.11%	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
vg0516242828	G -> A	LOC_Os05g27860.1	stop_gained ; p.Trp57*; HIGH	stop_gained	Average:21.772; most accessible tissue: Zhenshan97 flag leaf, score: 33.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516242828	NA	1.40E-14	Grain_width	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
vg0516242828	NA	1.27E-11	mr1540	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
vg0516242828	NA	3.04E-13	mr1732	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
vg0516242828	NA	4.07E-08	mr1800	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
vg0516242828	NA	2.87E-06	mr1423_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
vg0516242828	NA	7.63E-08	mr1446_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
vg0516242828	NA	4.52E-19	mr1539_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
vg0516242828	NA	1.11E-21	mr1540_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
vg0516242828	NA	2.88E-06	mr1540_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
vg0516242828	NA	5.92E-22	mr1732_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
vg0516242828	4.57E-06	1.34E-07	mr1732_2	Ind_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
vg0516242828	NA	9.84E-10	mr1771_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
vg0516242828	NA	9.55E-10	mr1784_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