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Detailed information for vg1002270223:

Variant ID: vg1002270223 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2270223
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATGCATTCAAAGTAGACATGATACCAGCAGATTTAAACAGTATCAGGTTTAACCAAAATCTTACCACTTCTAGCACAACACCTAACACAACAGGGGG[G/A]
TGTCTAGAATTATGAGCATAAGGATTAAAACCTAAACCACGGTTATGTGTGCTAACTTTAGATTGATCCAAAATCATGTTGAGGTTCTTTTTACCATCAG

Reverse complement sequence

CTGATGGTAAAAAGAACCTCAACATGATTTTGGATCAATCTAAAGTTAGCACACATAACCGTGGTTTAGGTTTTAATCCTTATGCTCATAATTCTAGACA[C/T]
CCCCCTGTTGTGTTAGGTGTTGTGCTAGAAGTGGTAAGATTTTGGTTAAACCTGATACTGTTTAAATCTGCTGGTATCATGTCTACTTTGAATGCATTTT

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	21.50%	19.70%	0.87%	57.98%	NA
All Indica	2759	3.20%	14.80%	0.98%	81.08%	NA
All Japonica	1512	59.60%	24.90%	0.40%	15.15%	NA
Aus	269	0.40%	13.40%	2.23%	84.01%	NA
Indica I	595	2.90%	31.30%	1.34%	64.54%	NA
Indica II	465	1.30%	2.80%	1.08%	94.84%	NA
Indica III	913	3.60%	14.20%	0.22%	81.93%	NA
Indica Intermediate	786	3.90%	10.10%	1.53%	84.48%	NA
Temperate Japonica	767	51.40%	39.80%	0.13%	8.74%	NA
Tropical Japonica	504	75.00%	3.20%	0.60%	21.23%	NA
Japonica Intermediate	241	53.50%	22.80%	0.83%	22.82%	NA
VI/Aromatic	96	9.40%	84.40%	0.00%	6.25%	NA
Intermediate	90	18.90%	32.20%	2.22%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002270223	G -> A	LOC_Os10g04740.1	intron_variant ; MODIFIER	silent_mutation	Average:10.281; most accessible tissue: Callus, score: 35.558	N	N	N	N
vg1002270223	G -> DEL	N	N	silent_mutation	Average:10.281; most accessible tissue: Callus, score: 35.558	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002270223	1.36E-06	NA	mr1218	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
vg1002270223	NA	7.54E-11	mr1709_2	Jap_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