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Detailed information for vg0718667525:

Variant ID: vg0718667525 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 18667525
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: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCATGTTATCACATCACTTTTGGTTCATACAAGGCAAGATGAAGTTCTGCATGTTTTGGATTCAAATTCAGACCTCCTAATAGCATTAACTTCAAAC[G/A]
GATCTAGTCGTTGATTTAAAAGGAATTTAGGGGCCTATGAGTACTTGTTGGAAAGCTTATGGAGTCTACTTTCAGATGGTTTTGGTCCCATGTAAAAATT

Reverse complement sequence

AATTTTTACATGGGACCAAAACCATCTGAAAGTAGACTCCATAAGCTTTCCAACAAGTACTCATAGGCCCCTAAATTCCTTTTAAATCAACGACTAGATC[C/T]
GTTTGAAGTTAATGCTATTAGGAGGTCTGAATTTGAATCCAAAACATGCAGAACTTCATCTTGCCTTGTATGAACCAAAAGTGATGTGATAACATGGGAG

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	51.20%	48.50%	0.28%	0.00%	NA
All Indica	2759	30.10%	69.40%	0.47%	0.00%	NA
All Japonica	1512	81.80%	18.20%	0.00%	0.00%	NA
Aus	269	78.80%	21.20%	0.00%	0.00%	NA
Indica I	595	19.50%	79.80%	0.67%	0.00%	NA
Indica II	465	7.50%	92.30%	0.22%	0.00%	NA
Indica III	913	46.40%	53.00%	0.55%	0.00%	NA
Indica Intermediate	786	32.40%	67.20%	0.38%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	57.50%	42.50%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	21.60%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	0.00%	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
vg0718667525	G -> A	LOC_Os07g31470-LOC_Os07g31480	intergenic_region ; MODIFIER	silent_mutation	Average:34.933; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0718667525	NA	1.20E-09	mr1180_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
vg0718667525	NA	1.65E-07	mr1183_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
vg0718667525	8.91E-06	NA	mr1226_2	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
vg0718667525	2.61E-06	1.31E-07	mr1480_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
vg0718667525	NA	2.16E-07	mr1885_2	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