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Detailed information for vg1201249880:

Variant ID: vg1201249880 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 1249880
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTCAAAATGTTATAAAGGTCCGGTTCATTTCCACTGCAAGGAGTGGATAAAGTTTTGGATTTTGATGACATGCTTTTCAAACTGCTAAACATTATATT[A/G]
AGCCATTTTTCAAGTTTGTACTCCCTCCGTTTCAAAATGTTTGACACCGTTGACTTTTTAGTACATGTTTGACCGTTCGTCTTATTCAAAAAAAATTTTG

Reverse complement sequence

CAAAATTTTTTTTGAATAAGACGAACGGTCAAACATGTACTAAAAAGTCAACGGTGTCAAACATTTTGAAACGGAGGGAGTACAAACTTGAAAAATGGCT[T/C]
AATATAATGTTTAGCAGTTTGAAAAGCATGTCATCAAAATCCAAAACTTTATCCACTCCTTGCAGTGGAAATGAACCGGACCTTTATAACATTTTGAGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.40%	12.30%	1.59%	0.76%	NA
All Indica	2759	75.50%	20.50%	2.68%	1.30%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	77.50%	21.00%	1.01%	0.50%	NA
Indica II	465	94.00%	5.20%	0.65%	0.22%	NA
Indica III	913	63.00%	28.70%	5.70%	2.63%	NA
Indica Intermediate	786	77.60%	19.70%	1.65%	1.02%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg1201249880	A -> DEL	N	N	silent_mutation	Average:41.477; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1201249880	A -> G	LOC_Os12g03250.1	upstream_gene_variant ; 3215.0bp to feature; MODIFIER	silent_mutation	Average:41.477; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1201249880	A -> G	LOC_Os12g03260.1	downstream_gene_variant ; 1271.0bp to feature; MODIFIER	silent_mutation	Average:41.477; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1201249880	A -> G	LOC_Os12g03250-LOC_Os12g03260	intergenic_region ; MODIFIER	silent_mutation	Average:41.477; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1201249880	2.57E-06	8.60E-06	Grain_weight	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