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Detailed information for vg0224652507:

Variant ID: vg0224652507 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24652507
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGTACAGAAGGGATTAGGTGAACTTTCGAGAGTACACAGGGGATTTTCTCTTTTTTTTTTCTTGACATCGAACTATTACCCTTGCGGTTTGTAGATGA[G/A]
GCGCATCGCATAGGCAGGTGACATAGAAATGTCTAGTACTAGTCAAGGTTGTCAGTATCCCGATTCATATCCTAGTATCTTACGATACTACGATACTACG

Reverse complement sequence

CGTAGTATCGTAGTATCGTAAGATACTAGGATATGAATCGGGATACTGACAACCTTGACTAGTACTAGACATTTCTATGTCACCTGCCTATGCGATGCGC[C/T]
TCATCTACAAACCGCAAGGGTAATAGTTCGATGTCAAGAAAAAAAAAAGAGAAAATCCCCTGTGTACTCTCGAAAGTTCACCTAATCCCTTCTGTACCCC

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	52.80%	3.60%	0.59%	43.00%	NA
All Indica	2759	37.10%	4.90%	0.58%	57.38%	NA
All Japonica	1512	85.50%	1.50%	0.00%	13.03%	NA
Aus	269	14.90%	1.90%	2.97%	80.30%	NA
Indica I	595	26.10%	0.00%	0.34%	73.61%	NA
Indica II	465	14.00%	9.50%	0.00%	76.56%	NA
Indica III	913	49.30%	5.60%	1.10%	44.03%	NA
Indica Intermediate	786	45.00%	5.20%	0.51%	49.24%	NA
Temperate Japonica	767	95.20%	0.10%	0.00%	4.69%	NA
Tropical Japonica	504	70.80%	2.60%	0.00%	26.59%	NA
Japonica Intermediate	241	85.50%	3.30%	0.00%	11.20%	NA
VI/Aromatic	96	86.50%	0.00%	3.12%	10.42%	NA
Intermediate	90	62.20%	7.80%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224652507	G -> A	LOC_Os02g40664.1	upstream_gene_variant ; 1303.0bp to feature; MODIFIER	silent_mutation	Average:25.478; most accessible tissue: Callus, score: 55.667	N	N	N	N
vg0224652507	G -> A	LOC_Os02g40664-LOC_Os02g40680	intergenic_region ; MODIFIER	silent_mutation	Average:25.478; most accessible tissue: Callus, score: 55.667	N	N	N	N
vg0224652507	G -> DEL	N	N	silent_mutation	Average:25.478; most accessible tissue: Callus, score: 55.667	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224652507	4.00E-06	3.99E-06	mr1341_2	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