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Detailed information for vg1224489196:

Variant ID: vg1224489196 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24489196
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

AATCAACTAGCAGATATTTCATGATTTATAATTTTTTATTCAAGTCATGCATTTAGTCAATTTATCCAGCACCATACACCCATACAAAACCTAAATATTG[G/A]
TAATCTGAAATATCCTTATTTATGTCATCCAGTAACTAATGCTTGCTTATTCAGGTGGCGAAAGAGAGTGCCGATGTCATAATTCTGGACGACAACTTCT

Reverse complement sequence

AGAAGTTGTCGTCCAGAATTATGACATCGGCACTCTCTTTCGCCACCTGAATAAGCAAGCATTAGTTACTGGATGACATAAATAAGGATATTTCAGATTA[C/T]
CAATATTTAGGTTTTGTATGGGTGTATGGTGCTGGATAAATTGACTAAATGCATGACTTGAATAAAAAATTATAAATCATGAAATATCTGCTAGTTGATT

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	94.10%	5.70%	0.17%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	83.50%	16.00%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.70%	2.70%	0.52%	0.00%	NA
Tropical Japonica	504	75.60%	24.00%	0.40%	0.00%	NA
Japonica Intermediate	241	57.70%	41.50%	0.83%	0.00%	NA
VI/Aromatic	96	72.90%	27.10%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1224489196	G -> A	LOC_Os12g39670.1	upstream_gene_variant ; 3333.0bp to feature; MODIFIER	silent_mutation	Average:49.126; most accessible tissue: Callus, score: 77.756	N	N	N	N
vg1224489196	G -> A	LOC_Os12g39660.1	intron_variant ; MODIFIER	silent_mutation	Average:49.126; most accessible tissue: Callus, score: 77.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224489196	NA	1.18E-08	Grain_weight	Jap_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