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Detailed information for vg0321809303:

Variant ID: vg0321809303 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21809303
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTCTTCACGGATCCTCAACTGGTGATAGCCTGATCGCAGGTCCATCTTAGGGAACACTGTAGCTCCTTTCAACTGATCAAACAGATCATCAATCCTTG[A/G]
CAAAGGGTACTTGTTCTTAATAGTGACCTCATTGAGTGCGTACTAGTTAACGCACATCCTCTTGGTTTTGTCTTTCTTTTCCACAAAGATTACCGGAGCA

Reverse complement sequence

TGCTCCGGTAATCTTTGTGGAAAAGAAAGACAAAACCAAGAGGATGTGCGTTAACTAGTACGCACTCAATGAGGTCACTATTAAGAACAAGTACCCTTTG[T/C]
CAAGGATTGATGATCTGTTTGATCAGTTGAAAGGAGCTACAGTGTTCCCTAAGATGGACCTGCGATCAGGCTATCACCAGTTGAGGATCCGTGAAGAGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.20%	24.50%	0.76%	42.59%	NA
All Indica	2759	4.30%	33.20%	1.16%	61.29%	NA
All Japonica	1512	89.70%	8.50%	0.00%	1.79%	NA
Aus	269	0.70%	0.40%	1.49%	97.40%	NA
Indica I	595	4.90%	72.60%	0.34%	22.18%	NA
Indica II	465	4.50%	12.70%	1.08%	81.72%	NA
Indica III	913	1.20%	28.60%	1.10%	69.11%	NA
Indica Intermediate	786	7.40%	21.00%	1.91%	69.72%	NA
Temperate Japonica	767	97.90%	2.00%	0.00%	0.13%	NA
Tropical Japonica	504	89.90%	5.20%	0.00%	4.96%	NA
Japonica Intermediate	241	63.50%	36.10%	0.00%	0.41%	NA
VI/Aromatic	96	2.10%	92.70%	0.00%	5.21%	NA
Intermediate	90	45.60%	23.30%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321809303	A -> DEL	LOC_Os03g39250.1	N	frameshift_variant	Average:46.128; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0321809303	A -> G	LOC_Os03g39250.1	missense_variant ; p.Ser606Pro; MODERATE	nonsynonymous_codon ; S606P	Average:46.128; most accessible tissue: Minghui63 flag leaf, score: 73.334	benign	-0.593	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321809303	NA	6.53E-08	mr1074	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
vg0321809303	NA	8.15E-07	mr1081	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
vg0321809303	8.01E-06	NA	mr1130	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
vg0321809303	NA	1.37E-10	mr1130	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
vg0321809303	NA	9.83E-10	mr1148	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
vg0321809303	NA	2.03E-07	mr1245	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
vg0321809303	NA	2.31E-07	mr1254	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
vg0321809303	NA	5.47E-06	mr1256	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
vg0321809303	NA	7.42E-06	mr1450	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
vg0321809303	NA	3.64E-06	mr1625	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
vg0321809303	NA	6.48E-07	mr1677	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
vg0321809303	NA	4.64E-06	mr1677	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
vg0321809303	9.06E-07	9.05E-07	mr1681	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
vg0321809303	NA	9.04E-07	mr1857	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