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Detailed information for vg0505358756:

Variant ID: vg0505358756 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5358756
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TACGCTTGTTTGTTTGTAGAGGGGAGCTTCCAGATGTGATTTTTACTGCCAAATAGATCTAACGATCTAAAATAATGGGTCCACCAATTTAAATGAAAAT[C/T]
AATGGTCGGATTTATTTTTTTTTATTAGAATGCCACTTGGCGACTCGATAGCGTTTATAGGAAGTTTAATGGACTTTTAGTATATAATAGATTATAGCTC

Reverse complement sequence

GAGCTATAATCTATTATATACTAAAAGTCCATTAAACTTCCTATAAACGCTATCGAGTCGCCAAGTGGCATTCTAATAAAAAAAAATAAATCCGACCATT[G/A]
ATTTTCATTTAAATTGGTGGACCCATTATTTTAGATCGTTAGATCTATTTGGCAGTAAAAATCACATCTGGAAGCTCCCCTCTACAAACAAACAAGCGTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.90%	31.00%	0.42%	1.71%	NA
All Indica	2759	53.90%	45.90%	0.22%	0.04%	NA
All Japonica	1512	88.70%	5.30%	0.73%	5.29%	NA
Aus	269	76.20%	22.70%	1.12%	0.00%	NA
Indica I	595	17.80%	81.50%	0.67%	0.00%	NA
Indica II	465	85.20%	14.80%	0.00%	0.00%	NA
Indica III	913	59.80%	40.00%	0.11%	0.11%	NA
Indica Intermediate	786	55.70%	44.10%	0.13%	0.00%	NA
Temperate Japonica	767	97.10%	1.80%	0.78%	0.26%	NA
Tropical Japonica	504	73.20%	11.90%	0.79%	14.09%	NA
Japonica Intermediate	241	94.20%	2.50%	0.41%	2.90%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0505358756	C -> T	LOC_Os05g09510-LOC_Os05g09520	intergenic_region ; MODIFIER	silent_mutation	Average:22.13; most accessible tissue: Callus, score: 36.907	N	N	N	N
vg0505358756	C -> DEL	N	N	silent_mutation	Average:22.13; most accessible tissue: Callus, score: 36.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505358756	7.73E-08	NA	Grain_length	All	YES	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
vg0505358756	1.23E-06	4.42E-26	Grain_length	Ind_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
vg0505358756	3.93E-06	NA	Grain_thickness	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
vg0505358756	2.45E-09	4.31E-17	Grain_thickness	Ind_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
vg0505358756	2.99E-13	NA	Grain_width	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
vg0505358756	8.92E-22	6.57E-46	Grain_width	Ind_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
vg0505358756	NA	3.95E-08	mr1183	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
vg0505358756	NA	4.03E-08	mr1503	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
vg0505358756	NA	1.73E-07	mr1183_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
vg0505358756	NA	5.18E-06	mr1319_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
vg0505358756	NA	1.20E-07	mr1330_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