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Detailed information for vg0523235966:

Variant ID: vg0523235966 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23235966
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAACCTGAAGCTTACAGAAATTACGGTGGCTAAAACAGACTCCAAGCAGCGGGAAGGGGCTAAGCCATGCTAAACTCCCAACAAATCCCCAAAAGCA[G/A]
CGACGCCAGCTAAAGACCACAGATGGCCCTCCACATGGACGGACTCCAAAACCACTGTGACCGAAGAGAGAGCGGAGTCGAAAACCCTAGAGTTCCGCTC

Reverse complement sequence

GAGCGGAACTCTAGGGTTTTCGACTCCGCTCTCTCTTCGGTCACAGTGGTTTTGGAGTCCGTCCATGTGGAGGGCCATCTGTGGTCTTTAGCTGGCGTCG[C/T]
TGCTTTTGGGGATTTGTTGGGAGTTTAGCATGGCTTAGCCCCTTCCCGCTGCTTGGAGTCTGTTTTAGCCACCGTAATTTCTGTAAGCTTCAGGTTTTTT

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	51.90%	47.00%	0.08%	0.97%	NA
All Indica	2759	30.50%	67.80%	0.07%	1.59%	NA
All Japonica	1512	98.50%	1.40%	0.00%	0.07%	NA
Aus	269	3.70%	96.30%	0.00%	0.00%	NA
Indica I	595	19.50%	78.30%	0.00%	2.18%	NA
Indica II	465	20.40%	77.80%	0.00%	1.72%	NA
Indica III	913	43.20%	56.00%	0.00%	0.88%	NA
Indica Intermediate	786	30.20%	67.70%	0.25%	1.91%	NA
Temperate Japonica	767	99.30%	0.50%	0.00%	0.13%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	40.60%	0.00%	0.00%	NA
Intermediate	90	62.20%	34.40%	2.22%	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
vg0523235966	G -> DEL	N	N	silent_mutation	Average:48.651; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0523235966	G -> A	LOC_Os05g39580.1	downstream_gene_variant ; 3236.0bp to feature; MODIFIER	silent_mutation	Average:48.651; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0523235966	G -> A	LOC_Os05g39570-LOC_Os05g39580	intergenic_region ; MODIFIER	silent_mutation	Average:48.651; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523235966	NA	1.06E-10	mr1336	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
vg0523235966	NA	2.45E-14	mr1579	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
vg0523235966	NA	1.24E-13	mr1653	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
vg0523235966	NA	4.64E-18	mr1336_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
vg0523235966	NA	5.43E-06	mr1336_2	Ind_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
vg0523235966	4.66E-06	4.66E-06	mr1537_2	Ind_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
vg0523235966	NA	1.62E-14	mr1579_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
vg0523235966	NA	3.31E-12	mr1641_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
vg0523235966	NA	1.01E-07	mr1681_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
vg0523235966	NA	2.02E-07	mr1683_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
vg0523235966	5.17E-06	5.17E-06	mr1727_2	Ind_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
vg0523235966	NA	3.80E-07	mr1824_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
vg0523235966	2.68E-06	1.02E-06	mr1890_2	Ind_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
vg0523235966	NA	1.99E-08	mr1921_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