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Detailed information for vg1222361978:

Variant ID: vg1222361978 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22361978
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCATAATCTTTAATTTATTTTGTTATTAGTCTACGTTTAATATTTTAAATGTGTGCTGGCATATCCGATGTGACACGCCAAAACTTTTCACTCTTAGA[T/C]
CTAAACACCCCCTAAACTGGCATAACCAAGGGCGAGGTCTTGAATATTGGGCAATTTGTTATTTCAGTATGACTAGCAATAATCGCGTGCTATGCTGCGC

Reverse complement sequence

GCGCAGCATAGCACGCGATTATTGCTAGTCATACTGAAATAACAAATTGCCCAATATTCAAGACCTCGCCCTTGGTTATGCCAGTTTAGGGGGTGTTTAG[A/G]
TCTAAGAGTGAAAAGTTTTGGCGTGTCACATCGGATATGCCAGCACACATTTAAAATATTAAACGTAGACTAATAACAAAATAAATTAAAGATTATGCCT

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	81.60%	17.50%	0.06%	0.87%	NA
All Indica	2759	69.20%	29.40%	0.11%	1.34%	NA
All Japonica	1512	99.40%	0.40%	0.00%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	80.20%	19.70%	0.17%	0.00%	NA
Indica II	465	78.70%	15.90%	0.22%	5.16%	NA
Indica III	913	53.60%	46.20%	0.11%	0.11%	NA
Indica Intermediate	786	73.40%	25.10%	0.00%	1.53%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	0.00%	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
vg1222361978	T -> C	LOC_Os12g36520.1	intron_variant ; MODIFIER	silent_mutation	Average:31.731; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1222361978	T -> DEL	N	N	silent_mutation	Average:31.731; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222361978	NA	1.48E-06	mr1925	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