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Detailed information for vg0321808235:

Variant ID: vg0321808235 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21808235
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGCTATGCGAACCTGCTCCACCAATGTGGGCTGTGCCTCTAGGGCAGCCACGAATCCGTGCTCAACTATACTAAGGTTCAGATGTTCCAAATCACGTT[T/G]
AACCTCACAACACAGTTTCTCTACCCATGCAACATTGCAGTAACTCTTCCTGCTTAAGGCGTCTGCTACCACATTAGCCTTGCCGGCATGATAGTGTATT

Reverse complement sequence

AATACACTATCATGCCGGCAAGGCTAATGTGGTAGCAGACGCCTTAAGCAGGAAGAGTTACTGCAATGTTGCATGGGTAGAGAAACTGTGTTGTGAGGTT[A/C]
AACGTGATTTGGAACATCTGAACCTTAGTATAGTTGAGCACGGATTCGTGGCTGCCCTAGAGGCACAGCCCACATTGGTGGAGCAGGTTCGCATAGCTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.50%	25.10%	3.89%	38.47%	NA
All Indica	2759	4.80%	34.10%	4.64%	56.51%	NA
All Japonica	1512	89.80%	8.50%	0.60%	1.06%	NA
Aus	269	1.10%	2.20%	15.61%	81.04%	NA
Indica I	595	5.40%	72.40%	1.85%	20.34%	NA
Indica II	465	4.50%	14.20%	4.95%	76.34%	NA
Indica III	913	1.90%	29.20%	4.93%	63.96%	NA
Indica Intermediate	786	7.90%	22.40%	6.23%	63.49%	NA
Temperate Japonica	767	97.90%	2.00%	0.00%	0.13%	NA
Tropical Japonica	504	89.90%	5.60%	1.79%	2.78%	NA
Japonica Intermediate	241	63.90%	35.70%	0.00%	0.41%	NA
VI/Aromatic	96	2.10%	92.70%	1.04%	4.17%	NA
Intermediate	90	46.70%	25.60%	4.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321808235	T -> DEL	LOC_Os03g39250.1	N	frameshift_variant	Average:43.517; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg0321808235	T -> G	LOC_Os03g39250.1	missense_variant ; p.Lys914Gln; MODERATE	nonsynonymous_codon ; K914Q	Average:43.517; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	benign	-0.99	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321808235	NA	4.88E-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
vg0321808235	NA	5.45E-08	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
vg0321808235	NA	2.75E-11	mr1130	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
vg0321808235	NA	5.37E-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
vg0321808235	NA	5.23E-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
vg0321808235	NA	1.24E-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
vg0321808235	NA	2.17E-06	mr1272	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
vg0321808235	NA	1.85E-06	mr1607	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
vg0321808235	NA	1.44E-06	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
vg0321808235	NA	5.03E-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
vg0321808235	NA	2.43E-06	mr1680	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
vg0321808235	NA	1.12E-06	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
vg0321808235	NA	8.51E-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