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Detailed information for vg0321809157:

Variant ID: vg0321809157 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21809157
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAAACCACGACAAACTTGTCTAGAAATTCCATAAACACCTTGTTCATCAAATTCATGAAGAAGGCAGGTTCGTTGGTGAGTCCGAAAGACATAACTGT[A/G]
CATTCGAACAACCCATAACAAGTGATGAATGCAGTCTTTGGAATATCCTCTTCACGGATCCTCAACTGGTGATAGCCTGATCGCAGGTCCATCTTAGGGA

Reverse complement sequence

TCCCTAAGATGGACCTGCGATCAGGCTATCACCAGTTGAGGATCCGTGAAGAGGATATTCCAAAGACTGCATTCATCACTTGTTATGGGTTGTTCGAATG[T/C]
ACAGTTATGTCTTTCGGACTCACCAACGAACCTGCCTTCTTCATGAATTTGATGAACAAGGTGTTTATGGAATTTCTAGACAAGTTTGTCGTGGTTTTCA

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	32.30%	24.30%	0.74%	42.64%	NA
All Indica	2759	4.50%	32.90%	1.23%	61.33%	NA
All Japonica	1512	89.80%	8.40%	0.00%	1.79%	NA
Aus	269	1.10%	0.70%	0.37%	97.77%	NA
Indica I	595	4.90%	72.10%	0.34%	22.69%	NA
Indica II	465	5.40%	12.70%	1.08%	80.86%	NA
Indica III	913	1.20%	28.40%	1.42%	69.00%	NA
Indica Intermediate	786	7.50%	20.60%	1.78%	70.10%	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	63.90%	35.70%	0.00%	0.41%	NA
VI/Aromatic	96	2.10%	92.70%	0.00%	5.21%	NA
Intermediate	90	44.40%	24.40%	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
vg0321809157	A -> DEL	LOC_Os03g39250.1	N	frameshift_variant	Average:42.553; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0321809157	A -> G	LOC_Os03g39250.1	synonymous_variant ; p.Cys654Cys; LOW	synonymous_codon	Average:42.553; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321809157	NA	8.22E-06	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
vg0321809157	NA	4.35E-06	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
vg0321809157	NA	3.44E-06	mr1189	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
vg0321809157	2.14E-06	NA	mr1229	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
vg0321809157	NA	1.31E-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
vg0321809157	NA	9.90E-06	mr1373	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
vg0321809157	NA	2.89E-06	mr1413	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
vg0321809157	NA	2.20E-07	mr1425	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
vg0321809157	NA	2.45E-07	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
vg0321809157	NA	2.36E-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
vg0321809157	NA	1.64E-07	mr1680	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
vg0321809157	NA	1.47E-06	mr1734	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
vg0321809157	NA	3.65E-06	mr1990	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
vg0321809157	NA	1.29E-06	mr1272_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