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Detailed information for vg0222703153:

Variant ID: vg0222703153 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22703153
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: 89. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCATTGAGTCGTACACAGTGACTCTGCATGCATCCAAGTCGAAGAATAACAGGACCCAGTGGAATCTAGAATATGCGTGAGATGAGATATATATGATC[G/A]
AAAATGTACATGCTATATGTATGGGAATGAAATTTGTTCGAACGACAATAAAAACTCACTCTGTGTTGTACGGCAGTAGTATGTACGTCTTGAAATGCTG

Reverse complement sequence

CAGCATTTCAAGACGTACATACTACTGCCGTACAACACAGAGTGAGTTTTTATTGTCGTTCGAACAAATTTCATTCCCATACATATAGCATGTACATTTT[C/T]
GATCATATATATCTCATCTCACGCATATTCTAGATTCCACTGGGTCCTGTTATTCTTCGACTTGGATGCATGCAGAGTCACTGTGTACGACTCAATGAAT

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	68.80%	1.80%	17.86%	11.57%	NA
All Indica	2759	51.60%	2.70%	27.00%	18.70%	NA
All Japonica	1512	99.80%	0.00%	0.20%	0.00%	NA
Aus	269	55.40%	3.30%	32.34%	8.92%	NA
Indica I	595	54.30%	0.80%	36.97%	7.90%	NA
Indica II	465	50.10%	0.20%	29.68%	20.00%	NA
Indica III	913	45.70%	5.60%	20.92%	27.82%	NA
Indica Intermediate	786	57.30%	2.30%	24.94%	15.52%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	82.20%	1.10%	8.89%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222703153	G -> A	LOC_Os02g37620.1	intron_variant ; MODIFIER	silent_mutation	Average:22.597; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg0222703153	G -> DEL	N	N	silent_mutation	Average:22.597; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222703153	1.33E-06	NA	mr1929	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
vg0222703153	3.86E-06	8.08E-08	mr1929	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