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Detailed information for vg0217843760:

Variant ID: vg0217843760 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17843760
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCGACTAGGTCATCGTGGCGAATGCCCTTGGTGAAGGCAGCGATGATGACGTCGTCGGTGATGTCGGAGATCTTGTTGCGTTGCTCGGAAAAGCGTCT[G/A]
ATGTAATCTCGAAGGGATTCTCTAGACTTCTGAACAACATTGTAGAGATCAAACTGTGTACTAGGGCGTTCAAAGATACCCTGGAAGTTGGCGATGAAGT

Reverse complement sequence

ACTTCATCGCCAACTTCCAGGGTATCTTTGAACGCCCTAGTACACAGTTTGATCTCTACAATGTTGTTCAGAAGTCTAGAGAATCCCTTCGAGATTACAT[C/T]
AGACGCTTTTCCGAGCAACGCAACAAGATCTCCGACATCACCGACGACGTCATCATCGCTGCCTTCACCAAGGGCATTCGCCACGATGACCTAGTCGGCA

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	73.00%	27.00%	0.02%	0.00%	NA
All Indica	2759	59.30%	40.60%	0.04%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	79.60%	20.40%	0.00%	0.00%	NA
Indica I	595	69.90%	30.10%	0.00%	0.00%	NA
Indica II	465	86.70%	13.30%	0.00%	0.00%	NA
Indica III	913	33.70%	66.20%	0.11%	0.00%	NA
Indica Intermediate	786	64.90%	35.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0217843760	G -> A	LOC_Os02g30040.1	synonymous_variant ; p.Ile474Ile; LOW	synonymous_codon	Average:53.328; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217843760	7.24E-07	5.12E-12	mr1317	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
vg0217843760	NA	5.29E-06	mr1317	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
vg0217843760	3.64E-06	3.02E-08	mr1610	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
vg0217843760	1.68E-07	NA	mr1855	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
vg0217843760	3.84E-06	5.65E-11	mr1317_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
vg0217843760	1.89E-06	2.44E-06	mr1608_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
vg0217843760	3.93E-06	NA	mr1610_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
vg0217843760	3.43E-06	NA	mr1818_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
vg0217843760	2.22E-08	NA	mr1855_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
vg0217843760	9.29E-06	NA	mr1897_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
vg0217843760	3.06E-07	NA	mr1914_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
vg0217843760	NA	3.99E-06	mr1914_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
vg0217843760	6.76E-07	NA	mr1927_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
vg0217843760	NA	5.01E-06	mr1927_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