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Detailed information for vg0134236787:

Variant ID: vg0134236787 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34236787
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCAGATATATTATGTTTCCACCAAATAATTCCATATGCGACCTGACTAGCCTGTTGCCGCTAGTCTACTCGCCCTTCGCACTTGCAAACTATCCATCT[G/A]
TAGAACCTTCTTGTCCTTCTTCTGGATCCGTTAACAAGTTCCTGCAACGAACCACACATCCGTTGAACCCGGTCTAACCGTCCAAACTCCGCAGTCTAAC

Reverse complement sequence

GTTAGACTGCGGAGTTTGGACGGTTAGACCGGGTTCAACGGATGTGTGGTTCGTTGCAGGAACTTGTTAACGGATCCAGAAGAAGGACAAGAAGGTTCTA[C/T]
AGATGGATAGTTTGCAAGTGCGAAGGGCGAGTAGACTAGCGGCAACAGGCTAGTCAGGTCGCATATGGAATTATTTGGTGGAAACATAATATATCTGGGA

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	85.30%	13.80%	0.06%	0.87%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	62.40%	34.90%	0.20%	2.51%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	88.40%	7.20%	0.00%	4.43%	NA
Tropical Japonica	504	34.10%	65.90%	0.00%	0.00%	NA
Japonica Intermediate	241	38.60%	58.50%	1.24%	1.66%	NA
VI/Aromatic	96	10.40%	86.50%	0.00%	3.12%	NA
Intermediate	90	66.70%	33.30%	0.00%	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
vg0134236787	G -> A	LOC_Os01g59230.1	intron_variant ; MODIFIER	silent_mutation	Average:62.444; most accessible tissue: Zhenshan97 flower, score: 78.317	N	N	N	N
vg0134236787	G -> DEL	N	N	silent_mutation	Average:62.444; most accessible tissue: Zhenshan97 flower, score: 78.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134236787	NA	5.63E-10	mr1128	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
vg0134236787	NA	4.63E-06	mr1503	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
vg0134236787	7.93E-07	NA	mr1679	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
vg0134236787	4.57E-07	NA	mr1691	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
vg0134236787	1.52E-06	NA	mr1691	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
vg0134236787	9.32E-07	NA	mr1720	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
vg0134236787	9.04E-06	NA	mr1720	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
vg0134236787	NA	3.90E-08	mr1084_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
vg0134236787	NA	2.70E-08	mr1180_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
vg0134236787	NA	1.04E-06	mr1183_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
vg0134236787	NA	3.82E-07	mr1350_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
vg0134236787	NA	7.05E-06	mr1383_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
vg0134236787	NA	1.11E-06	mr1691_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