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Detailed information for vg1215352517:

Variant ID: vg1215352517 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15352517
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.01, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCCATACAAGTCCTAGGAGCATTCTTAGAAATCTTGTGCCTAACACCCTCAGTCATCCACTTTACATAAGGAGTTCCCTTCCTAGTAGTACCAAAGAA[T/A]
GCTGTCGCATAGAACTGTGCAATGACCTCCTCATTCCAATCATACTCCAAGGCAAGAATATCCCCAAGATTCTTGTTGTGGCAAACTTGCATTGCTTGAT

Reverse complement sequence

ATCAAGCAATGCAAGTTTGCCACAACAAGAATCTTGGGGATATTCTTGCCTTGGAGTATGATTGGAATGAGGAGGTCATTGCACAGTTCTATGCGACAGC[A/T]
TTCTTTGGTACTACTAGGAAGGGAACTCCTTATGTAAAGTGGATGACTGAGGGTGTTAGGCACAAGATTTCTAAGAATGCTCCTAGGACTTGTATGGGAA

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	85.20%	2.90%	3.13%	8.82%	NA
All Indica	2759	93.10%	2.40%	1.67%	2.83%	NA
All Japonica	1512	79.50%	0.90%	0.66%	18.92%	NA
Aus	269	46.80%	20.10%	31.60%	1.49%	NA
Indica I	595	90.90%	3.20%	2.18%	3.70%	NA
Indica II	465	95.30%	0.60%	1.08%	3.01%	NA
Indica III	913	95.40%	1.80%	1.20%	1.64%	NA
Indica Intermediate	786	91.00%	3.40%	2.16%	3.44%	NA
Temperate Japonica	767	94.00%	0.00%	0.13%	5.87%	NA
Tropical Japonica	504	59.30%	2.60%	0.99%	37.10%	NA
Japonica Intermediate	241	75.50%	0.40%	1.66%	22.41%	NA
VI/Aromatic	96	51.00%	0.00%	5.21%	43.75%	NA
Intermediate	90	86.70%	3.30%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215352517	T -> DEL	LOC_Os12g26310.1	N	frameshift_variant	Average:9.854; most accessible tissue: Callus, score: 18.344	N	N	N	N
vg1215352517	T -> A	LOC_Os12g26310.1	synonymous_variant ; p.Ala1661Ala; LOW	synonymous_codon	Average:9.854; most accessible tissue: Callus, score: 18.344	N	N	N	N
vg1215352517	T -> A	LOC_Os12g26310.1	synonymous_variant ; p.Ala1661Ala; LOW	nonsynonymous_codon ; A1661T	Average:9.854; most accessible tissue: Callus, score: 18.344	unknown	unknown	TOLERATED	0.12

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215352517	7.23E-07	NA	Plant_height	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1215352517	NA	8.36E-07	mr1651	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