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Detailed information for vg0614456600:

Variant ID: vg0614456600 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14456600
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

CAAATTATCAATTAATTAACATAACACAACACGATTAACCATCGTGAGCTACCAATAATTATAATCATAATTAATAATAATATAATATAATATATATTTA[G/A]
TCCCCTTTAATTAGCTAATGTTTCTAAGCATGACTAAGCAAACATACATATAGCATTTAGCTGAACCAATCCAATATATAAGGTTCATGCTAATCAAATT

Reverse complement sequence

AATTTGATTAGCATGAACCTTATATATTGGATTGGTTCAGCTAAATGCTATATGTATGTTTGCTTAGTCATGCTTAGAAACATTAGCTAATTAAAGGGGA[C/T]
TAAATATATATTATATTATATTATTATTAATTATGATTATAATTATTGGTAGCTCACGATGGTTAATCGTGTTGTGTTATGTTAATTAATTGATAATTTG

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	40.60%	0.30%	27.32%	31.76%	NA
All Indica	2759	7.70%	0.40%	44.47%	47.48%	NA
All Japonica	1512	91.30%	0.10%	0.60%	7.94%	NA
Aus	269	70.60%	0.00%	11.90%	17.47%	NA
Indica I	595	13.90%	0.00%	17.98%	68.07%	NA
Indica II	465	4.50%	0.40%	39.14%	55.91%	NA
Indica III	913	1.60%	0.50%	67.69%	30.12%	NA
Indica Intermediate	786	11.80%	0.40%	40.71%	47.07%	NA
Temperate Japonica	767	96.30%	0.10%	0.52%	3.00%	NA
Tropical Japonica	504	82.90%	0.20%	0.79%	16.07%	NA
Japonica Intermediate	241	92.90%	0.00%	0.41%	6.64%	NA
VI/Aromatic	96	88.50%	2.10%	6.25%	3.12%	NA
Intermediate	90	57.80%	0.00%	18.89%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614456600	G -> A	LOC_Os06g24620.1	upstream_gene_variant ; 1215.0bp to feature; MODIFIER	silent_mutation	Average:16.427; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0614456600	G -> A	LOC_Os06g24630.1	upstream_gene_variant ; 3807.0bp to feature; MODIFIER	silent_mutation	Average:16.427; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0614456600	G -> A	LOC_Os06g24610-LOC_Os06g24620	intergenic_region ; MODIFIER	silent_mutation	Average:16.427; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0614456600	G -> DEL	N	N	silent_mutation	Average:16.427; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614456600	2.90E-06	NA	mr1993_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