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Detailed information for vg0224797537:

Variant ID: vg0224797537 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24797537
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: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CATCTGGTGAAGCAAACAAAACTATGTGGCCCGGCTTTTCTAAGGGAAATGTGGTCGTTTGAAAGGTACATGGGAGTTCTGAAGTCGTACGTTCATAACA[G/A]
AGCTAAACCCGAGGGGAGCATCATTGAAGGTTACACGACCGAGGAGGCTATTGAGTTCTGTGTCAATTACATGTCCGATGCCGATCCTATCGGAGTTCCT

Reverse complement sequence

AGGAACTCCGATAGGATCGGCATCGGACATGTAATTGACACAGAACTCAATAGCCTCCTCGGTCGTGTAACCTTCAATGATGCTCCCCTCGGGTTTAGCT[C/T]
TGTTATGAACGTACGACTTCAGAACTCCCATGTACCTTTCAAACGACCACATTTCCCTTAGAAAAGCCGGGCCACATAGTTTTGTTTGCTTCACCAGATG

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	73.60%	25.90%	0.47%	0.00%	NA
All Indica	2759	89.20%	10.50%	0.25%	0.00%	NA
All Japonica	1512	49.40%	49.90%	0.66%	0.00%	NA
Aus	269	50.20%	49.40%	0.37%	0.00%	NA
Indica I	595	97.60%	2.00%	0.34%	0.00%	NA
Indica II	465	77.40%	22.60%	0.00%	0.00%	NA
Indica III	913	94.20%	5.70%	0.11%	0.00%	NA
Indica Intermediate	786	84.10%	15.40%	0.51%	0.00%	NA
Temperate Japonica	767	65.80%	33.50%	0.65%	0.00%	NA
Tropical Japonica	504	24.00%	75.40%	0.60%	0.00%	NA
Japonica Intermediate	241	50.20%	49.00%	0.83%	0.00%	NA
VI/Aromatic	96	75.00%	22.90%	2.08%	0.00%	NA
Intermediate	90	71.10%	26.70%	2.22%	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
vg0224797537	G -> A	LOC_Os02g40920.1	missense_variant ; p.Arg571Lys; MODERATE	nonsynonymous_codon ; R571K	Average:21.62; most accessible tissue: Minghui63 root, score: 29.362	benign	1.391	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224797537	4.66E-06	6.14E-08	mr1042_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
vg0224797537	NA	5.94E-07	mr1150_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
vg0224797537	NA	7.26E-06	mr1185_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
vg0224797537	NA	7.01E-06	mr1269_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
vg0224797537	NA	2.44E-06	mr1269_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
vg0224797537	NA	8.41E-07	mr1291_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
vg0224797537	NA	1.94E-07	mr1479_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
vg0224797537	1.09E-06	1.29E-08	mr1479_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
vg0224797537	NA	1.40E-07	mr1502_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
vg0224797537	NA	7.26E-06	mr1543_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
vg0224797537	6.07E-06	6.11E-08	mr1871_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
vg0224797537	8.92E-06	5.66E-08	mr1892_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
vg0224797537	4.66E-06	4.66E-06	mr1919_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