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Detailed information for vg0312437905:

Variant ID: vg0312437905 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 12437905
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.33, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGCAATGAGACACGGCGCGCTCGGCCATCTTCTGCCCGAACGAGAGCATCTCAGCGGCCAAATTCTCCACCGTGGGGTCGCCAAACCCCTCGTCCAAC[A/G]
CGGCAGCGGTGGCGGCGATCGGCCTCTACCACCACATTCGTTCGTACCACGCGCACGGCCAGCTCCATGCCTAGCCACTCCCCTTGACACCGGTCATGAG

Reverse complement sequence

CTCATGACCGGTGTCAAGGGGAGTGGCTAGGCATGGAGCTGGCCGTGCGCGTGGTACGAACGAATGTGGTGGTAGAGGCCGATCGCCGCCACCGCTGCCG[T/C]
GTTGGACGAGGGGTTTGGCGACCCCACGGTGGAGAATTTGGCCGCTGAGATGCTCTCGTTCGGGCAGAAGATGGCCGAGCGCGCCGTGTCTCATTGCCGA

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	60.30%	39.40%	0.11%	0.23%	NA
All Indica	2759	92.10%	7.50%	0.14%	0.25%	NA
All Japonica	1512	1.70%	98.10%	0.07%	0.13%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	84.20%	15.80%	0.00%	0.00%	NA
Indica II	465	97.80%	1.70%	0.00%	0.43%	NA
Indica III	913	95.70%	4.10%	0.00%	0.22%	NA
Indica Intermediate	786	90.60%	8.50%	0.51%	0.38%	NA
Temperate Japonica	767	0.50%	99.30%	0.00%	0.13%	NA
Tropical Japonica	504	3.00%	96.80%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.10%	0.00%	0.41%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	47.80%	50.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0312437905	A -> DEL	N	N	silent_mutation	Average:68.315; most accessible tissue: Zhenshan97 young leaf, score: 89.339	N	N	N	N
vg0312437905	A -> G	LOC_Os03g21759.1	upstream_gene_variant ; 157.0bp to feature; MODIFIER	silent_mutation	Average:68.315; most accessible tissue: Zhenshan97 young leaf, score: 89.339	N	N	N	N
vg0312437905	A -> G	LOC_Os03g21770.1	upstream_gene_variant ; 2758.0bp to feature; MODIFIER	silent_mutation	Average:68.315; most accessible tissue: Zhenshan97 young leaf, score: 89.339	N	N	N	N
vg0312437905	A -> G	LOC_Os03g21750.1	downstream_gene_variant ; 3829.0bp to feature; MODIFIER	silent_mutation	Average:68.315; most accessible tissue: Zhenshan97 young leaf, score: 89.339	N	N	N	N
vg0312437905	A -> G	LOC_Os03g21759-LOC_Os03g21770	intergenic_region ; MODIFIER	silent_mutation	Average:68.315; most accessible tissue: Zhenshan97 young leaf, score: 89.339	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0312437905	5.53E-07	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