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Detailed information for vg1200352652:

Variant ID: vg1200352652 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 352652
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAATTCCTTACTTTAAGGGCATATGGTGCACCGCCAGTCATAGTAGCGCTTGCAGCACAAGGTGCTTTTCGTGGATTCATGGATACAAAGACACCGTT[G/A]
TTTGCTGTGGGTAAGACAATGTATGCAAACTCTTCTGGATGAAATAATTGGTTTTAGGGTGCTTTTCAATTCTTCCGTCTTCCATTTGGACTTGCTAGTT

Reverse complement sequence

AACTAGCAAGTCCAAATGGAAGACGGAAGAATTGAAAAGCACCCTAAAACCAATTATTTCATCCAGAAGAGTTTGCATACATTGTCTTACCCACAGCAAA[C/T]
AACGGTGTCTTTGTATCCATGAATCCACGAAAAGCACCTTGTGCTGCAAGCGCTACTATGACTGGCGGTGCACCATATGCCCTTAAAGTAAGGAATTGCT

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	79.90%	19.90%	0.08%	0.15%	NA
All Indica	2759	68.00%	31.70%	0.11%	0.22%	NA
All Japonica	1512	96.80%	3.10%	0.00%	0.07%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	95.00%	5.00%	0.00%	0.00%	NA
Indica II	465	26.50%	72.70%	0.00%	0.86%	NA
Indica III	913	72.70%	27.10%	0.11%	0.11%	NA
Indica Intermediate	786	66.70%	33.00%	0.25%	0.13%	NA
Temperate Japonica	767	95.60%	4.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.00%	0.00%	0.20%	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	82.20%	16.70%	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
vg1200352652	G -> DEL	LOC_Os12g01580.2	N	frameshift_variant	Average:53.669; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg1200352652	G -> DEL	LOC_Os12g01580.1	N	frameshift_variant	Average:53.669; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg1200352652	G -> A	LOC_Os12g01580.1	synonymous_variant ; p.Leu274Leu; LOW	synonymous_codon	Average:53.669; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg1200352652	G -> A	LOC_Os12g01580.2	synonymous_variant ; p.Leu63Leu; LOW	synonymous_codon	Average:53.669; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200352652	NA	9.36E-17	Grain_length	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
vg1200352652	NA	8.33E-18	Grain_length	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
vg1200352652	NA	2.10E-09	mr1174	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
vg1200352652	NA	4.02E-09	mr1174_2	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