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Detailed information for vg1215484344:

Variant ID: vg1215484344 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15484344
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGAGCATGTCATACTATAATCGATAGTGAGAGTTGCAATAACTTTGTGAGTTTAGATTTGGTTGAGAAACTTGAGTGGCTTACACAACCGCATCCTCA[T/A]
CCATATTACATCAAATGGTTCAACTCTTGTGGTAAGTTCAAGGTAAATAGAACTGTGAGAATAAACTTTTCGATTGGAGATTACCATGAAGCTGCCAATT

Reverse complement sequence

AATTGGCAGCTTCATGGTAATCTCCAATCGAAAAGTTTATTCTCACAGTTCTATTTACCTTGAACTTACCACAAGAGTTGAACCATTTGATGTAATATGG[A/T]
TGAGGATGCGGTTGTGTAAGCCACTCAAGTTTCTCAACCAAATCTAAACTCACAAAGTTATTGCAACTCTCACTATCGATTATAGTATGACATGCTCTAT

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	95.00%	2.30%	1.46%	1.18%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	88.00%	4.90%	3.70%	3.44%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	98.30%	0.30%	1.17%	0.26%	NA
Tropical Japonica	504	76.00%	9.90%	7.34%	6.75%	NA
Japonica Intermediate	241	80.10%	9.10%	4.15%	6.64%	NA
VI/Aromatic	96	57.30%	31.20%	7.29%	4.17%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215484344	T -> DEL	N	N	silent_mutation	Average:17.241; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg1215484344	T -> A	LOC_Os12g26480-LOC_Os12g26500	intergenic_region ; MODIFIER	silent_mutation	Average:17.241; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215484344	NA	8.05E-07	mr1308	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
vg1215484344	NA	7.97E-09	mr1584	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
vg1215484344	NA	2.40E-06	mr1072_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
vg1215484344	NA	2.56E-06	mr1075_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
vg1215484344	NA	1.62E-06	mr1124_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