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Detailed information for vg1014251223:

Variant ID: vg1014251223 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14251223
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCTTTTCGCCCCCCGCCCTGTTCACGGCACCTTGCTGCGAGTACGGCGTGGCAAAGGGCTAAATCACGGCTTGCGCGTGAGGTTGGGCCATGGCATTC[G/A]
GCTGCCCCGCTCCGATTGGTAATGCTTGCTGAGCCACCATGGAGGGGTCGAAAGTTGGCTGTGACCATGTCATGGCGACCTGGTTTGGTGCCTGGTTTGC

Reverse complement sequence

GCAAACCAGGCACCAAACCAGGTCGCCATGACATGGTCACAGCCAACTTTCGACCCCTCCATGGTGGCTCAGCAAGCATTACCAATCGGAGCGGGGCAGC[C/T]
GAATGCCATGGCCCAACCTCACGCGCAAGCCGTGATTTAGCCCTTTGCCACGCCGTACTCGCAGCAAGGTGCCGTGAACAGGGCGGGGGGCGAAAAGGGG

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	39.70%	0.20%	11.64%	48.43%	NA
All Indica	2759	7.80%	0.20%	12.14%	79.81%	NA
All Japonica	1512	99.30%	0.00%	0.07%	0.60%	NA
Aus	269	2.60%	1.50%	76.95%	18.96%	NA
Indica I	595	4.40%	0.00%	17.98%	77.65%	NA
Indica II	465	6.70%	0.00%	6.45%	86.88%	NA
Indica III	913	8.20%	0.40%	11.72%	79.63%	NA
Indica Intermediate	786	10.70%	0.30%	11.58%	77.48%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	64.40%	0.00%	5.56%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014251223	G -> A	LOC_Os10g27050.1	upstream_gene_variant ; 4546.0bp to feature; MODIFIER	silent_mutation	Average:49.359; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1014251223	G -> A	LOC_Os10g27040.1	intron_variant ; MODIFIER	silent_mutation	Average:49.359; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1014251223	G -> DEL	N	N	silent_mutation	Average:49.359; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014251223	4.90E-06	4.90E-06	mr1276	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