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Detailed information for vg0219500936:

Variant ID: vg0219500936 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19500936
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTATCTTATGTTAGCATGCGAGTTTTTTAAAGCGATATCTTATACGAGTCCTTTTGTATTTCTAACAGCGAACGAACTTAAAATCCGACTCAAATAT[G/A]
AATCTGTATATTCAAAATCGAACAAACTTAAAAATCAACTCATACATGGATGACATACCAAAGTACTAGCAGGGGCGGATTCACAATGGGGGCGGTGGGG

Reverse complement sequence

CCCCACCGCCCCCATTGTGAATCCGCCCCTGCTAGTACTTTGGTATGTCATCCATGTATGAGTTGATTTTTAAGTTTGTTCGATTTTGAATATACAGATT[C/T]
ATATTTGAGTCGGATTTTAAGTTCGTTCGCTGTTAGAAATACAAAAGGACTCGTATAAGATATCGCTTTAAAAAACTCGCATGCTAACATAAGATAATTG

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	74.30%	24.70%	0.93%	0.04%	NA
All Indica	2759	61.70%	37.00%	1.27%	0.07%	NA
All Japonica	1512	99.20%	0.60%	0.20%	0.00%	NA
Aus	269	72.50%	27.10%	0.37%	0.00%	NA
Indica I	595	53.30%	44.50%	2.18%	0.00%	NA
Indica II	465	77.80%	21.70%	0.22%	0.22%	NA
Indica III	913	51.50%	47.40%	0.99%	0.11%	NA
Indica Intermediate	786	70.20%	28.20%	1.53%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	47.90%	49.00%	3.12%	0.00%	NA
Intermediate	90	78.90%	18.90%	2.22%	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
vg0219500936	G -> A	LOC_Os02g32850.1	upstream_gene_variant ; 2564.0bp to feature; MODIFIER	silent_mutation	Average:43.825; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N
vg0219500936	G -> A	LOC_Os02g32840-LOC_Os02g32850	intergenic_region ; MODIFIER	silent_mutation	Average:43.825; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N
vg0219500936	G -> DEL	N	N	silent_mutation	Average:43.825; most accessible tissue: Zhenshan97 root, score: 57.64	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219500936	NA	4.99E-06	mr1590	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
vg0219500936	NA	6.88E-06	mr1837	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
vg0219500936	4.13E-06	4.13E-06	mr1994	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
vg0219500936	NA	9.54E-06	mr1255_2	Ind_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