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Detailed information for vg1209892012:

Variant ID: vg1209892012 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9892012
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACACATTCCCAAAGCTAAGGGATCACTGGGACGAGTTCGTTGCATATAAGACAAGTCAACAAGGGCAGGCGATGTTGGAAAGAAACAAAGAAAATGC[C/T]
GCTAAGAAGAAGTACCATCACCACTTGGGGTCAGGCGGCTATAGCGTCGCGATGCCGAAGTGGGAGGAGATGGAGGCAAGCTTGCTTGAGAGGGGTATCA

Reverse complement sequence

TGATACCCCTCTCAAGCAAGCTTGCCTCCATCTCCTCCCACTTCGGCATCGCGACGCTATAGCCGCCTGACCCCAAGTGGTGATGGTACTTCTTCTTAGC[G/A]
GCATTTTCTTTGTTTCTTTCCAACATCGCCTGCCCTTGTTGACTTGTCTTATATGCAACGAACTCGTCCCAGTGATCCCTTAGCTTTGGGAATGTGTCGA

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	54.30%	1.60%	40.22%	3.85%	NA
All Indica	2759	43.50%	2.60%	47.37%	6.52%	NA
All Japonica	1512	79.70%	0.00%	20.24%	0.07%	NA
Aus	269	27.10%	0.00%	72.86%	0.00%	NA
Indica I	595	34.80%	0.50%	56.30%	8.40%	NA
Indica II	465	55.10%	1.50%	34.19%	9.25%	NA
Indica III	913	43.40%	4.80%	48.41%	3.40%	NA
Indica Intermediate	786	43.40%	2.30%	47.20%	7.12%	NA
Temperate Japonica	767	88.70%	0.00%	11.21%	0.13%	NA
Tropical Japonica	504	70.00%	0.00%	29.96%	0.00%	NA
Japonica Intermediate	241	71.40%	0.00%	28.63%	0.00%	NA
VI/Aromatic	96	34.40%	3.10%	62.50%	0.00%	NA
Intermediate	90	62.20%	1.10%	35.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209892012	C -> DEL	LOC_Os12g17290.1	N	frameshift_variant	Average:52.245; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg1209892012	C -> T	LOC_Os12g17290.1	synonymous_variant ; p.Ala297Ala; LOW	synonymous_codon	Average:52.245; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209892012	2.68E-06	8.09E-08	mr1864	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
vg1209892012	NA	2.97E-08	mr1002_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