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Detailed information for vg1215889308:

Variant ID: vg1215889308 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15889308
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, A: 0.23, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAGCCAACATATGATTAATTTGGTTTTGGGATCTCTGTATCTTCTTTATAACAATTTCCCTCTCACCAAGTATCAGGCATTTGATCTCCCCGAAGATA[T/A]
GCAATCTTTCCTTTGTCGTATACGCCTCCGTCAAGAACAATATCATTAGAGCAATGTGATGAGCACCCAACAACGAGTACCCTAATTTATCCCCCTCTTT

Reverse complement sequence

AAAGAGGGGGATAAATTAGGGTACTCGTTGTTGGGTGCTCATCACATTGCTCTAATGATATTGTTCTTGACGGAGGCGTATACGACAAAGGAAAGATTGC[A/T]
TATCTTCGGGGAGATCAAATGCCTGATACTTGGTGAGAGGGAAATTGTTATAAAGAAGATACAGAGATCCCAAAACCAAATTAATCATATGTTGGCTCAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.00%	35.20%	0.80%	9.01%	NA
All Indica	2759	34.50%	58.50%	1.12%	5.91%	NA
All Japonica	1512	86.40%	1.30%	0.26%	11.97%	NA
Aus	269	69.90%	1.10%	1.12%	27.88%	NA
Indica I	595	16.30%	83.50%	0.17%	0.00%	NA
Indica II	465	55.70%	18.30%	1.29%	24.73%	NA
Indica III	913	29.50%	67.70%	1.53%	1.31%	NA
Indica Intermediate	786	41.50%	52.70%	1.27%	4.58%	NA
Temperate Japonica	767	99.20%	0.50%	0.00%	0.26%	NA
Tropical Japonica	504	64.50%	2.40%	0.79%	32.34%	NA
Japonica Intermediate	241	91.70%	1.70%	0.00%	6.64%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	67.80%	25.60%	0.00%	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
vg1215889308	T -> DEL	N	N	silent_mutation	Average:39.301; most accessible tissue: Zhenshan97 root, score: 85.556	N	N	N	N
vg1215889308	T -> A	LOC_Os12g27096.1	intron_variant ; MODIFIER	silent_mutation	Average:39.301; most accessible tissue: Zhenshan97 root, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215889308	NA	8.13E-06	mr1220_2	Jap_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
vg1215889308	6.44E-07	1.83E-07	mr1929_2	Jap_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