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Detailed information for vg1220855520:

Variant ID: vg1220855520 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20855520
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAGTTGCTTTGGTGAAGCTAACCGGCGGGTGAAAGTTTTGTTATCCTAACCCCCGCCGAGTTAGTCCGTTCTTGTTCCTTTGTGCAGAATGAGGAGGT[G/A]
ACTGTCTCGTCTATTTAAGAAGGGACCCGGCTCTCCATCAAGTCATCATGATGAGTCTAGCACTCGTTCATCTGCCGACGTCTCGATGGAGGACGCTAAT

Reverse complement sequence

ATTAGCGTCCTCCATCGAGACGTCGGCAGATGAACGAGTGCTAGACTCATCATGATGACTTGATGGAGAGCCGGGTCCCTTCTTAAATAGACGAGACAGT[C/T]
ACCTCCTCATTCTGCACAAAGGAACAAGAACGGACTAACTCGGCGGGGGTTAGGATAACAAAACTTTCACCCGCCGGTTAGCTTCACCAAAGCAACTTGT

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	88.60%	7.70%	1.80%	1.97%	NA
All Indica	2759	83.10%	12.70%	2.72%	1.45%	NA
All Japonica	1512	99.50%	0.30%	0.20%	0.00%	NA
Aus	269	78.80%	0.00%	1.86%	19.33%	NA
Indica I	595	96.50%	0.30%	3.19%	0.00%	NA
Indica II	465	62.40%	34.20%	3.01%	0.43%	NA
Indica III	913	89.90%	6.80%	0.99%	2.30%	NA
Indica Intermediate	786	77.40%	16.30%	4.20%	2.16%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	93.30%	5.60%	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
vg1220855520	G -> DEL	N	N	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1220855520	G -> A	LOC_Os12g34400.1	downstream_gene_variant ; 4262.0bp to feature; MODIFIER	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1220855520	G -> A	LOC_Os12g34410.1	downstream_gene_variant ; 786.0bp to feature; MODIFIER	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1220855520	G -> A	LOC_Os12g34419.1	downstream_gene_variant ; 839.0bp to feature; MODIFIER	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1220855520	G -> A	LOC_Os12g34430.1	downstream_gene_variant ; 2665.0bp to feature; MODIFIER	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1220855520	G -> A	LOC_Os12g34410-LOC_Os12g34419	intergenic_region ; MODIFIER	silent_mutation	Average:59.449; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220855520	5.33E-06	NA	mr1232	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220855520	4.00E-06	6.10E-08	mr1232	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251