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Detailed information for vg0140349681:

Variant ID: vg0140349681 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 40349681
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCATATTTCTTACCTAATTTGCATCTCTACCTTTGGACCACAAACTCTTAGTCTACAACTGCACATACCACTATCAAGCATGCCAGAAGGTATGATGT[G/A]
AGGACTATCGCAAATCACGTCTATAGTAGAAAAAAAAATCATGCCATATAAGGTTCATGGAGCACATGAAGGCAACCATGATATGGATGATGATGATGAC

Reverse complement sequence

GTCATCATCATCATCCATATCATGGTTGCCTTCATGTGCTCCATGAACCTTATATGGCATGATTTTTTTTTCTACTATAGACGTGATTTGCGATAGTCCT[C/T]
ACATCATACCTTCTGGCATGCTTGATAGTGGTATGTGCAGTTGTAGACTAAGAGTTTGTGGTCCAAAGGTAGAGATGCAAATTAGGTAAGAAATATGCGA

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	38.40%	32.90%	1.57%	27.13%	NA
All Indica	2759	9.00%	50.50%	2.10%	38.42%	NA
All Japonica	1512	97.60%	1.10%	0.33%	1.06%	NA
Aus	269	16.40%	11.90%	2.60%	69.14%	NA
Indica I	595	4.40%	78.50%	3.53%	13.61%	NA
Indica II	465	3.40%	7.30%	2.37%	86.88%	NA
Indica III	913	11.10%	66.50%	0.66%	21.80%	NA
Indica Intermediate	786	13.40%	36.30%	2.54%	47.84%	NA
Temperate Japonica	767	98.30%	0.90%	0.52%	0.26%	NA
Tropical Japonica	504	97.40%	0.60%	0.00%	1.98%	NA
Japonica Intermediate	241	95.40%	2.50%	0.41%	1.66%	NA
VI/Aromatic	96	7.30%	89.60%	1.04%	2.08%	NA
Intermediate	90	47.80%	28.90%	3.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0140349681	G -> A	LOC_Os01g69850.1	intron_variant ; MODIFIER	silent_mutation	Average:27.393; most accessible tissue: Callus, score: 80.334	N	N	N	N
vg0140349681	G -> DEL	N	N	silent_mutation	Average:27.393; most accessible tissue: Callus, score: 80.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0140349681	3.55E-06	NA	Heading_date	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