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Detailed information for vg0114524872:

Variant ID: vg0114524872 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14524872
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, C: 0.33, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAACTTAGAGCATTCTATAGAAGTAATTTAGTCAAATTTGAAAGTAACTTATATATATTATAAAAGTAACTTAGTATATAATAAAAGTAATTTACAA[C/A]
TATAAATATTTTTTCATTGTAATATAATCATGTAAGATCTTATTGTGAAGATTTAATTGTAACGAACATAATGGTGTAATTGGATTGTAAATCGGATAAG

Reverse complement sequence

CTTATCCGATTTACAATCCAATTACACCATTATGTTCGTTACAATTAAATCTTCACAATAAGATCTTACATGATTATATTACAATGAAAAAATATTTATA[G/T]
TTGTAAATTACTTTTATTATATACTAAGTTACTTTTATAATATATATAAGTTACTTTCAAATTTGACTAAATTACTTCTATAGAATGCTCTAAGTTAATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	15.20%	0.23%	4.85%	NA
All Indica	2759	68.30%	23.20%	0.40%	8.08%	NA
All Japonica	1512	97.50%	2.40%	0.00%	0.07%	NA
Aus	269	87.00%	11.50%	0.00%	1.49%	NA
Indica I	595	80.50%	14.50%	0.34%	4.71%	NA
Indica II	465	81.30%	13.30%	0.00%	5.38%	NA
Indica III	913	55.20%	36.00%	0.55%	8.21%	NA
Indica Intermediate	786	66.70%	20.70%	0.51%	12.09%	NA
Temperate Japonica	767	98.70%	1.20%	0.00%	0.13%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114524872	C -> A	LOC_Os01g25630.1	downstream_gene_variant ; 1730.0bp to feature; MODIFIER	silent_mutation	Average:20.284; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0114524872	C -> A	LOC_Os01g25610-LOC_Os01g25630	intergenic_region ; MODIFIER	silent_mutation	Average:20.284; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0114524872	C -> DEL	N	N	silent_mutation	Average:20.284; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114524872	1.40E-06	1.28E-10	Grain_thickness	Ind_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
vg0114524872	NA	4.61E-07	Grain_weight	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
vg0114524872	NA	5.03E-07	mr1042	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
vg0114524872	NA	1.74E-06	mr1043	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