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Detailed information for vg0711746376:

Variant ID: vg0711746376 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11746376
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.28, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCACTATAGTATAAACATGAATCAAATATATTACAATGAAGTAATAAGGATTCATGATTTCAAATGATTTATAATGCAATATATTCACAAGCACATAG[G/A]
TTGAAAAATAAACACTATACATATATACCTATTGCATTTATCACTCTTTCTCAAATTAGCTTTAGCACAAAACAATCAAGAGATTTTTTTTAACTTTTAT

Reverse complement sequence

ATAAAAGTTAAAAAAAATCTCTTGATTGTTTTGTGCTAAAGCTAATTTGAGAAAGAGTGATAAATGCAATAGGTATATATGTATAGTGTTTATTTTTCAA[C/T]
CTATGTGCTTGTGAATATATTGCATTATAAATCATTTGAAATCATGAATCCTTATTACTTCATTGTAATATATTTGATTCATGTTTATACTATAGTGCAT

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	96.50%	0.20%	0.93%	2.41%	NA
All Indica	2759	99.60%	0.20%	0.18%	0.07%	NA
All Japonica	1512	90.70%	0.10%	1.98%	7.21%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.30%	0.64%	0.25%	NA
Temperate Japonica	767	82.90%	0.10%	3.78%	13.17%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	96.30%	0.40%	0.41%	2.90%	NA
VI/Aromatic	96	86.50%	2.10%	8.33%	3.12%	NA
Intermediate	90	100.00%	0.00%	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
vg0711746376	G -> DEL	N	N	silent_mutation	Average:26.624; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0711746376	G -> A	LOC_Os07g20360.1	intron_variant ; MODIFIER	silent_mutation	Average:26.624; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711746376	2.47E-06	6.19E-06	mr1767_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