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Detailed information for vg0414319578:

Variant ID: vg0414319578 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14319578
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: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CTAACATTTTAAAATAAGGTCCACCGGTTTGGGTAAGATTTTTTTTCTCAAAATTTTTTATATAAAGATATATTAGAGCGTCATGTGGTGATTTAGGAAC[G/A]
TTTATGGGAAGCCACGTGGTAGCTTGAGAGAATTTGTAGGATATCTAACGGATCTTTAGTATATAATAATAGATAATTCATGTCATATTAATTAACATAT

Reverse complement sequence

ATATGTTAATTAATATGACATGAATTATCTATTATTATATACTAAAGATCCGTTAGATATCCTACAAATTCTCTCAAGCTACCACGTGGCTTCCCATAAA[C/T]
GTTCCTAAATCACCACATGACGCTCTAATATATCTTTATATAAAAAATTTTGAGAAAAAAAATCTTACCCAAACCGGTGGACCTTATTTTAAAATGTTAG

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	64.20%	29.60%	1.84%	4.32%	NA
All Indica	2759	54.20%	41.30%	2.54%	1.96%	NA
All Japonica	1512	77.40%	13.00%	0.86%	8.80%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	52.40%	36.60%	5.38%	5.55%	NA
Indica II	465	83.90%	13.50%	2.37%	0.22%	NA
Indica III	913	36.90%	61.10%	1.20%	0.77%	NA
Indica Intermediate	786	58.10%	38.20%	2.04%	1.65%	NA
Temperate Japonica	767	88.40%	2.70%	0.91%	7.95%	NA
Tropical Japonica	504	73.80%	17.50%	0.99%	7.74%	NA
Japonica Intermediate	241	49.80%	36.10%	0.41%	13.69%	NA
VI/Aromatic	96	44.80%	42.70%	2.08%	10.42%	NA
Intermediate	90	67.80%	22.20%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414319578	G -> DEL	N	N	silent_mutation	Average:7.445; most accessible tissue: Zhenshan97 flower, score: 15.748	N	N	N	N
vg0414319578	G -> A	LOC_Os04g24850-LOC_Os04g24860	intergenic_region ; MODIFIER	silent_mutation	Average:7.445; most accessible tissue: Zhenshan97 flower, score: 15.748	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414319578	NA	4.12E-06	mr1380_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
vg0414319578	2.55E-07	2.55E-07	mr1651_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