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Detailed information for vg1212666466:

Variant ID: vg1212666466 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12666466
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.26, others allele: 0.00, population size: 39. )

Flanking Sequence (100 bp) in Reference Genome:

GACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAG[T/C]
AGGTATGTTTCAACTGTTACAAGCCAGGTCACTTTGCAAGAGAATGTCCGAAGCCCAAGCATCAGCAGCCGCAAGGTCAAGTCAACAACATTGTCGTCAC

Reverse complement sequence

GTGACGACAATGTTGTTGACTTGACCTTGCGGCTGCTGATGCTTGGGCTTCGGACATTCTCTTGCAAAGTGACCTGGCTTGTAACAGTTGAAACATACCT[A/G]
CTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	16.70%	3.50%	14.09%	65.72%	NA
All Indica	2759	3.60%	5.90%	21.46%	68.97%	NA
All Japonica	1512	43.80%	0.10%	0.79%	55.29%	NA
Aus	269	0.40%	0.40%	18.22%	81.04%	NA
Indica I	595	0.70%	2.90%	11.26%	85.21%	NA
Indica II	465	3.40%	4.30%	25.16%	67.10%	NA
Indica III	913	3.80%	9.30%	26.18%	60.68%	NA
Indica Intermediate	786	5.70%	5.30%	21.50%	67.43%	NA
Temperate Japonica	767	77.80%	0.00%	0.52%	21.64%	NA
Tropical Japonica	504	1.80%	0.20%	0.79%	97.22%	NA
Japonica Intermediate	241	23.70%	0.00%	1.66%	74.69%	NA
VI/Aromatic	96	1.00%	0.00%	4.17%	94.79%	NA
Intermediate	90	24.40%	1.10%	10.00%	64.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1212666466	T -> C	LOC_Os12g22430.1	stop_lost&splice_region_variant ; p.Ter311Glnext*?; HIGH	stop_lost	Average:6.769; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1212666466	T -> DEL	LOC_Os12g22430.1	N	frameshift_variant	Average:6.769; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212666466	NA	7.66E-15	mr1156	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
vg1212666466	NA	2.94E-17	mr1013_2	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