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Detailed information for vg0407808783:

Variant ID: vg0407808783 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7808783
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCGGCGTCGATGCGGACATCCTCTGGTGCATATCGCGCTAGACGATTAAACTCATGGAGGTACTCAGTCACCGTCCGGTTGCCCTGGTGGAGTGCCCA[G/A]
AATTCTCTCTTCTTTTGTGGCACGACCCCGTCGGGCACCTGCGCCTTCCTAAAGCTGCGACAGAACTCCGCCCAAGTGACCTCCGTACCTGGCGGACGGG

Reverse complement sequence

CCCGTCCGCCAGGTACGGAGGTCACTTGGGCGGAGTTCTGTCGCAGCTTTAGGAAGGCGCAGGTGCCCGACGGGGTCGTGCCACAAAAGAAGAGAGAATT[C/T]
TGGGCACTCCACCAGGGCAACCGGACGGTGACTGAGTACCTCCATGAGTTTAATCGTCTAGCGCGATATGCACCAGAGGATGTCCGCATCGACGCCGAGA

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	80.60%	8.50%	10.83%	0.00%	NA
All Indica	2759	67.60%	14.40%	18.01%	0.00%	NA
All Japonica	1512	99.50%	0.20%	0.26%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	66.60%	8.60%	24.87%	0.00%	NA
Indica II	465	83.70%	6.50%	9.89%	0.00%	NA
Indica III	913	57.60%	22.60%	19.82%	0.00%	NA
Indica Intermediate	786	70.50%	14.00%	15.52%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	88.90%	3.30%	7.78%	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
vg0407808783	G -> A	LOC_Os04g13970.1	synonymous_variant ; p.Phe79Phe; LOW	synonymous_codon	Average:27.119; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407808783	7.08E-06	7.08E-06	mr1883	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
vg0407808783	4.88E-06	4.88E-06	mr1416_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