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Detailed information for vg0619448815:

Variant ID: vg0619448815 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19448815
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: 108. )

Flanking Sequence (100 bp) in Reference Genome:

AGACGTGGAGGGAGAAGAAAGAGAGTGGGGTGAGGGGTGAGGGACATATATGATAGGTGGGTCTCACCAATTTGTTTTCGAAGAAAATGTTAACTGGACT[G/A]
TCACGTAGGACCAAAACCAACTTGGGTTGAGTCAGCGGGTAATTTGTCTAATATTAATAATAGTTGAAGATGAAAGATGTTTGACTTTTGGGTTTATGGA

Reverse complement sequence

TCCATAAACCCAAAAGTCAAACATCTTTCATCTTCAACTATTATTAATATTAGACAAATTACCCGCTGACTCAACCCAAGTTGGTTTTGGTCCTACGTGA[C/T]
AGTCCAGTTAACATTTTCTTCGAAAACAAATTGGTGAGACCCACCTATCATATATGTCCCTCACCCCTCACCCCACTCTCTTTCTTCTCCCTCCACGTCT

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	87.80%	0.80%	2.56%	8.87%	NA
All Indica	2759	83.50%	1.10%	3.73%	11.71%	NA
All Japonica	1512	99.20%	0.30%	0.20%	0.33%	NA
Aus	269	95.90%	0.00%	1.49%	2.60%	NA
Indica I	595	83.40%	0.30%	2.35%	13.95%	NA
Indica II	465	97.20%	0.00%	1.08%	1.72%	NA
Indica III	913	75.70%	2.50%	7.12%	14.68%	NA
Indica Intermediate	786	84.50%	0.60%	2.42%	12.47%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.20%	0.20%	0.40%	0.20%	NA
Japonica Intermediate	241	97.10%	1.20%	0.41%	1.24%	NA
VI/Aromatic	96	9.40%	2.10%	9.38%	79.17%	NA
Intermediate	90	86.70%	2.20%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619448815	G -> A	LOC_Os06g33390.1	upstream_gene_variant ; 2292.0bp to feature; MODIFIER	silent_mutation	Average:71.379; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0619448815	G -> A	LOC_Os06g33380.1	downstream_gene_variant ; 4949.0bp to feature; MODIFIER	silent_mutation	Average:71.379; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0619448815	G -> A	LOC_Os06g33400.1	downstream_gene_variant ; 68.0bp to feature; MODIFIER	silent_mutation	Average:71.379; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0619448815	G -> A	LOC_Os06g33400-LOC_Os06g33410	intergenic_region ; MODIFIER	silent_mutation	Average:71.379; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0619448815	G -> DEL	N	N	silent_mutation	Average:71.379; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619448815	NA	1.74E-06	mr1107	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