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Detailed information for vg0311304375:

Variant ID: vg0311304375 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11304375
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CCACTTCGCCATCGATGCAGGTACTAGCCAAGCATCTGAACGCTCCGGCCGCAGCATGAAATTCACACAGCCGAAAACGGTTTTCCTCGGACCCGCCGGC[G/A]
TCTGCACGTCTTTGGTCGAGGCGCATGCAGTAAACAGAGCGGCAAATAGCTCAGCGGTAGGGACGAACCCACAGGTTCGGCACATCCAAGCGAAAACCGC

Reverse complement sequence

GCGGTTTTCGCTTGGATGTGCCGAACCTGTGGGTTCGTCCCTACCGCTGAGCTATTTGCCGCTCTGTTTACTGCATGCGCCTCGACCAAAGACGTGCAGA[C/T]
GCCGGCGGGTCCGAGGAAAACCGTTTTCGGCTGTGTGAATTTCATGCTGCGGCCGGAGCGTTCAGATGCTTGGCTAGTACCTGCATCGATGGCGAAGTGG

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	60.10%	15.30%	2.64%	21.98%	NA
All Indica	2759	35.40%	25.50%	3.91%	35.19%	NA
All Japonica	1512	99.50%	0.10%	0.13%	0.26%	NA
Aus	269	72.50%	4.50%	4.09%	18.96%	NA
Indica I	595	51.40%	10.60%	0.84%	37.14%	NA
Indica II	465	4.30%	61.10%	4.09%	30.54%	NA
Indica III	913	38.70%	16.10%	5.15%	40.09%	NA
Indica Intermediate	786	37.90%	26.60%	4.71%	30.79%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	8.90%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0311304375	G -> A	LOC_Os03g20070.1	upstream_gene_variant ; 3235.0bp to feature; MODIFIER	silent_mutation	Average:48.141; most accessible tissue: Zhenshan97 flag leaf, score: 78.259	N	N	N	N
vg0311304375	G -> A	LOC_Os03g20050.1	downstream_gene_variant ; 3621.0bp to feature; MODIFIER	silent_mutation	Average:48.141; most accessible tissue: Zhenshan97 flag leaf, score: 78.259	N	N	N	N
vg0311304375	G -> A	LOC_Os03g20060.1	intron_variant ; MODIFIER	silent_mutation	Average:48.141; most accessible tissue: Zhenshan97 flag leaf, score: 78.259	N	N	N	N
vg0311304375	G -> DEL	N	N	silent_mutation	Average:48.141; most accessible tissue: Zhenshan97 flag leaf, score: 78.259	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311304375	NA	3.15E-06	mr1064	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
vg0311304375	NA	1.51E-06	mr1090	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
vg0311304375	NA	2.68E-12	mr1329	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
vg0311304375	NA	6.19E-07	mr1378	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
vg0311304375	NA	4.50E-06	mr1520	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
vg0311304375	NA	1.20E-11	mr1524	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
vg0311304375	NA	1.18E-07	mr1629	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
vg0311304375	NA	1.74E-09	mr1637	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
vg0311304375	NA	5.82E-06	mr1731	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
vg0311304375	NA	1.80E-06	mr1887	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
vg0311304375	NA	6.68E-07	mr1974	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
vg0311304375	NA	1.18E-06	mr1974	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
vg0311304375	NA	3.19E-06	mr1232_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
vg0311304375	NA	1.55E-07	mr1347_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
vg0311304375	NA	1.28E-07	mr1527_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
vg0311304375	NA	1.47E-07	mr1557_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
vg0311304375	9.07E-07	NA	mr1581_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
vg0311304375	NA	2.21E-08	mr1659_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