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Detailed information for vg0407808726:

Variant ID: vg0407808726 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7808726
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGAGATTAACTGGTTGGTCAGCTCGTCATCCAGGCCTGCTAGGAACTTCTCCTGTTTCTCGGCGTCGATGCGGACATCCTCTGGTGCATATCGCGCTAG[A/G]
CGATTAAACTCATGGAGGTACTCAGTCACCGTCCGGTTGCCCTGGTGGAGTGCCCAGAATTCTCTCTTCTTTTGTGGCACGACCCCGTCGGGCACCTGCG

Reverse complement sequence

CGCAGGTGCCCGACGGGGTCGTGCCACAAAAGAAGAGAGAATTCTGGGCACTCCACCAGGGCAACCGGACGGTGACTGAGTACCTCCATGAGTTTAATCG[T/C]
CTAGCGCGATATGCACCAGAGGATGTCCGCATCGACGCCGAGAAACAGGAGAAGTTCCTAGCAGGCCTGGATGACGAGCTGACCAACCAGTTAATCTCTG

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	60.30%	39.20%	0.47%	0.00%	NA
All Indica	2759	90.10%	9.20%	0.69%	0.00%	NA
All Japonica	1512	1.30%	98.70%	0.00%	0.00%	NA
Aus	269	97.40%	1.50%	1.12%	0.00%	NA
Indica I	595	86.40%	12.80%	0.84%	0.00%	NA
Indica II	465	86.50%	12.00%	1.51%	0.00%	NA
Indica III	913	97.70%	1.80%	0.55%	0.00%	NA
Indica Intermediate	786	86.30%	13.50%	0.25%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	44.40%	55.60%	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
vg0407808726	A -> G	LOC_Os04g13970.1	synonymous_variant ; p.Arg98Arg; LOW	synonymous_codon	Average:27.254; 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
vg0407808726	NA	9.38E-11	mr1553	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
vg0407808726	NA	4.34E-09	mr1379_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
vg0407808726	NA	1.58E-19	mr1416_2	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