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Detailed information for vg0112932528:

Variant ID: vg0112932528 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12932528
Reference Allele: A	Alternative Allele: G,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TCACGGGTAGAAAATCTTCCCCATACCCATACCCGTGCGGGTAACGGGTATCCAACGGGTACCTATACCCATATAGTTGACTTGTAGCATTTATAGTTTT[A/G,T]
TACTGTAATTAGCCATATTAGAGTTGTAAACCATCAATATTTTCTCGAGCAACAATCTATTAACATTAGCGTTCAAAGGTAAGTAAAAAAATTATACAAC

Reverse complement sequence

GTTGTATAATTTTTTTACTTACCTTTGAACGCTAATGTTAATAGATTGTTGCTCGAGAAAATATTGATGGTTTACAACTCTAATATGGCTAATTACAGTA[T/C,A]
AAAACTATAAATGCTACAAGTCAACTATATGGGTATAGGTACCCGTTGGATACCCGTTACCCGCACGGGTATGGGTATGGGGAAGATTTTCTACCCGTGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.40%	25.60%	0.02%	0.00%	T: 0.02%
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	24.90%	75.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.00%	0.00%	T: 0.37%
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	23.20%	76.80%	0.00%	0.00%	NA
Tropical Japonica	504	36.30%	63.70%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	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
vg0112932528	A -> G	LOC_Os01g23000.1	splice_region_variant&synonymous_variant ; p.Tyr155Tyr; LOW	synonymous_codon	Average:71.037; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N
vg0112932528	A -> T	LOC_Os01g23000.1	stop_gained&splice_region_variant ; p.Tyr155*; HIGH	stop_gained	Average:71.037; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112932528	NA	2.58E-08	mr1648	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
vg0112932528	NA	1.86E-21	mr1010_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
vg0112932528	1.84E-06	4.38E-12	mr1030_2	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
vg0112932528	NA	6.31E-07	mr1030_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
vg0112932528	NA	6.27E-13	mr1035_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
vg0112932528	NA	5.97E-07	mr1097_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
vg0112932528	NA	8.22E-06	mr1154_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
vg0112932528	NA	8.55E-15	mr1162_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
vg0112932528	NA	2.63E-07	mr1164_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
vg0112932528	NA	1.58E-06	mr1358_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
vg0112932528	NA	2.79E-06	mr1444_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
vg0112932528	NA	8.08E-11	mr1576_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
vg0112932528	NA	4.06E-09	mr1709_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
vg0112932528	NA	6.34E-17	mr1712_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
vg0112932528	NA	5.33E-08	mr1749_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
vg0112932528	NA	3.25E-06	mr1754_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
vg0112932528	NA	1.33E-10	mr1761_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
vg0112932528	NA	1.50E-12	mr1770_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
vg0112932528	NA	7.00E-08	mr1821_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
vg0112932528	NA	6.55E-06	mr1982_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