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Detailed information for vg0413702577:

Variant ID: vg0413702577 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13702577
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATCATGTTTGCCATGGTTTGAAAAATCAAAATTGCTCTTGTGAAATGTATGATAAGACAATGGTTAGAAAGTATAAGATTTTCTGCTCCTGTTGAGT[G/A]
CACTTCTCTGATTACTCGGATAGCAAAAGGGCTAGGGGTCGTTAGTGACCAGATTGCTTTTATCTCAGCCGCTTGTCCGTGTATTGACGAAAATTATTTA

Reverse complement sequence

TAAATAATTTTCGTCAATACACGGACAAGCGGCTGAGATAAAAGCAATCTGGTCACTAACGACCCCTAGCCCTTTTGCTATCCGAGTAATCAGAGAAGTG[C/T]
ACTCAACAGGAGCAGAAAATCTTATACTTTCTAACCATTGTCTTATCATACATTTCACAAGAGCAATTTTGATTTTTCAAACCATGGCAAACATGATAAT

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	97.40%	1.20%	1.40%	0.00%	NA
All Indica	2759	99.40%	0.20%	0.43%	0.00%	NA
All Japonica	1512	93.20%	3.40%	3.44%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.30%	1.01%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.40%	0.76%	0.00%	NA
Temperate Japonica	767	88.10%	6.50%	5.35%	0.00%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0413702577	G -> A	LOC_Os04g23960.1	downstream_gene_variant ; 2119.0bp to feature; MODIFIER	silent_mutation	Average:26.434; most accessible tissue: Minghui63 flag leaf, score: 41.254	N	N	N	N
vg0413702577	G -> A	LOC_Os04g23980.1	downstream_gene_variant ; 3747.0bp to feature; MODIFIER	silent_mutation	Average:26.434; most accessible tissue: Minghui63 flag leaf, score: 41.254	N	N	N	N
vg0413702577	G -> A	LOC_Os04g23970.1	intron_variant ; MODIFIER	silent_mutation	Average:26.434; most accessible tissue: Minghui63 flag leaf, score: 41.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413702577	2.32E-06	2.32E-06	mr1717	Jap_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