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Detailed information for vg1215556442:

Variant ID: vg1215556442 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15556442
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGTTAGACCGCCGAAACCCAGTAAACACAAATCGAAGAACTCTTAAAGTGGATGACGACTTTATTGATTCTCTCTGTATTTACAAAGTGCACCAACAA[C/G]
ACTCCTTACAAAAATTTCGACTAAACTCGAAACCCTAACTCAAAACTCAACTCAATTGCTCTCTAAAGCGATAATGGGAAGCCTCACGCTCCCCCCTCTA

Reverse complement sequence

TAGAGGGGGGAGCGTGAGGCTTCCCATTATCGCTTTAGAGAGCAATTGAGTTGAGTTTTGAGTTAGGGTTTCGAGTTTAGTCGAAATTTTTGTAAGGAGT[G/C]
TTGTTGGTGCACTTTGTAAATACAGAGAGAATCAATAAAGTCGTCATCCACTTTAAGAGTTCTTCGATTTGTGTTTACTGGGTTTCGGCGGTCTAACCGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.40%	18.70%	4.57%	20.25%	NA
All Indica	2759	39.40%	31.10%	6.16%	23.27%	NA
All Japonica	1512	82.70%	0.90%	1.98%	14.42%	NA
Aus	269	81.40%	0.40%	2.60%	15.61%	NA
Indica I	595	18.30%	61.30%	9.58%	10.76%	NA
Indica II	465	58.70%	12.50%	4.09%	24.73%	NA
Indica III	913	42.10%	19.70%	4.93%	33.30%	NA
Indica Intermediate	786	41.00%	32.60%	6.23%	20.23%	NA
Temperate Japonica	767	96.60%	0.40%	0.52%	2.48%	NA
Tropical Japonica	504	63.50%	1.20%	3.77%	31.55%	NA
Japonica Intermediate	241	78.80%	1.70%	2.90%	16.60%	NA
VI/Aromatic	96	49.00%	1.00%	8.33%	41.67%	NA
Intermediate	90	68.90%	13.30%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215556442	C -> DEL	N	N	silent_mutation	Average:9.632; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1215556442	C -> G	LOC_Os12g26580.1	upstream_gene_variant ; 766.0bp to feature; MODIFIER	silent_mutation	Average:9.632; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1215556442	C -> G	LOC_Os12g26580-LOC_Os12g26590	intergenic_region ; MODIFIER	silent_mutation	Average:9.632; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215556442	2.08E-06	NA	mr1659	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
vg1215556442	4.12E-07	5.37E-08	mr1659	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