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Detailed information for vg1216184823:

Variant ID: vg1216184823 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16184823
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GAGAATGACATCTAGGTCTTTAGATTCGAGAAGGATGAGGTTGGATAGAAACGGTGATCTTTTGATCTCTATAGTCACCGAGGGGCAATAGTGTGATGTC[C/T]
TCATGTCATTTCCAGGGGTATGAACCTGCATCGGTATTTTAAGTTCCACTACCGATAATCCATGTGTCCCAGCAAATCTTTTGGAAATGAAAGAATGCGA

Reverse complement sequence

TCGCATTCTTTCATTTCCAAAAGATTTGCTGGGACACATGGATTATCGGTAGTGGAACTTAAAATACCGATGCAGGTTCATACCCCTGGAAATGACATGA[G/A]
GACATCACACTATTGCCCCTCGGTGACTATAGAGATCAAAAGATCACCGTTTCTATCCAACCTCATCCTTCTCGAATCTAAAGACCTAGATGTCATTCTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.30%	0.30%	35.48%	11.89%	NA
All Indica	2759	21.20%	0.50%	58.83%	19.46%	NA
All Japonica	1512	98.30%	0.00%	1.39%	0.26%	NA
Aus	269	88.10%	0.00%	6.32%	5.58%	NA
Indica I	595	20.00%	0.50%	54.96%	24.54%	NA
Indica II	465	18.90%	0.00%	47.74%	33.33%	NA
Indica III	913	19.50%	1.00%	73.60%	5.91%	NA
Indica Intermediate	786	25.30%	0.40%	51.15%	23.16%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	96.00%	0.00%	3.57%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	76.70%	1.10%	15.56%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216184823	C -> DEL	LOC_Os12g27490.1	N	frameshift_variant	Average:14.497; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N
vg1216184823	C -> T	LOC_Os12g27490.1	missense_variant ; p.Arg559Lys; MODERATE	nonsynonymous_codon ; R559K	Average:14.497; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	unknown	unknown	TOLERATED	0.22

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216184823	8.58E-08	2.02E-07	mr1946	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
vg1216184823	NA	8.86E-06	mr1547_2	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