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Detailed information for vg1213457856:

Variant ID: vg1213457856 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13457856
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

CACTTTAAGAGAAGGAGGTATTTCCAGACCCTATAGAACTGGAAAATATTATGACAGTTGTTAGCAGCAACAATTGAATTTGTCGGCCTAGAATGCGCCA[C/A]
AGTCATATTACCTATGGAACAATTGTGCACTTTTTAGAAGCATCTATTGTCCGTCAACCCCGTTGAACTCTCTAAAGAGTGTGATGTTTCAAGCTACACC

Reverse complement sequence

GGTGTAGCTTGAAACATCACACTCTTTAGAGAGTTCAACGGGGTTGACGGACAATAGATGCTTCTAAAAAGTGCACAATTGTTCCATAGGTAATATGACT[G/T]
TGGCGCATTCTAGGCCGACAAATTCAATTGTTGCTGCTAACAACTGTCATAATATTTTCCAGTTCTATAGGGTCTGGAAATACCTCCTTCTCTTAAAGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.30%	23.60%	19.36%	29.73%	NA
All Indica	2759	44.90%	13.30%	23.92%	17.94%	NA
All Japonica	1512	1.80%	46.10%	5.69%	46.43%	NA
Aus	269	1.10%	6.30%	44.98%	47.58%	NA
Indica I	595	35.50%	11.30%	26.72%	26.55%	NA
Indica II	465	37.60%	17.80%	19.57%	24.95%	NA
Indica III	913	57.60%	8.50%	24.32%	9.53%	NA
Indica Intermediate	786	41.50%	17.60%	23.92%	17.05%	NA
Temperate Japonica	767	1.20%	78.40%	2.09%	18.38%	NA
Tropical Japonica	504	3.60%	6.00%	10.32%	80.16%	NA
Japonica Intermediate	241	0.00%	27.40%	7.47%	65.15%	NA
VI/Aromatic	96	6.20%	2.10%	28.12%	63.54%	NA
Intermediate	90	20.00%	35.60%	23.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213457856	C -> DEL	N	N	silent_mutation	Average:16.71; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213457856	C -> A	LOC_Os12g23720.1	upstream_gene_variant ; 2876.0bp to feature; MODIFIER	silent_mutation	Average:16.71; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213457856	C -> A	LOC_Os12g23720-LOC_Os12g23730	intergenic_region ; MODIFIER	silent_mutation	Average:16.71; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213457856	NA	6.59E-07	mr1425	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
vg1213457856	NA	1.08E-07	mr1425	Ind_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
vg1213457856	NA	1.96E-09	mr1910_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