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Detailed information for vg0420836195:

Variant ID: vg0420836195 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20836195
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTTTCTAAGAAGTTGGGGGGAGGCAGTTTTGGTTCTGTATTTAGAGCAATGCTCCGGTGCTTTCTACCGGTAGTATATACTACCAGTAGAACTAATCT[G/A]
AACCGTTTATTTTTAAGGGTAGATTAGTAAAGTACTGAGGTAGATTTGGGATAAATTTGGCACTTAATTTATTTTTGTCGTGGATCGCTCGGATGTTTCT

Reverse complement sequence

AGAAACATCCGAGCGATCCACGACAAAAATAAATTAAGTGCCAAATTTATCCCAAATCTACCTCAGTACTTTACTAATCTACCCTTAAAAATAAACGGTT[C/T]
AGATTAGTTCTACTGGTAGTATATACTACCGGTAGAAAGCACCGGAGCATTGCTCTAAATACAGAACCAAAACTGCCTCCCCCCAACTTCTTAGAAAAGT

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	27.10%	15.10%	32.25%	25.50%	NA
All Indica	2759	7.90%	24.90%	45.78%	21.42%	NA
All Japonica	1512	65.00%	0.40%	3.84%	30.75%	NA
Aus	269	2.60%	0.40%	52.04%	44.98%	NA
Indica I	595	2.70%	9.90%	44.71%	42.69%	NA
Indica II	465	13.30%	44.10%	20.22%	22.37%	NA
Indica III	913	6.90%	24.50%	62.76%	5.81%	NA
Indica Intermediate	786	9.90%	25.20%	41.98%	22.90%	NA
Temperate Japonica	767	82.80%	0.30%	1.04%	15.91%	NA
Tropical Japonica	504	36.90%	0.80%	8.53%	53.77%	NA
Japonica Intermediate	241	67.20%	0.00%	2.90%	29.88%	NA
VI/Aromatic	96	37.50%	11.50%	38.54%	12.50%	NA
Intermediate	90	41.10%	12.20%	28.89%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420836195	G -> DEL	N	N	silent_mutation	Average:55.277; most accessible tissue: Minghui63 flag leaf, score: 66.556	N	N	N	N
vg0420836195	G -> A	LOC_Os04g34410.1	intron_variant ; MODIFIER	silent_mutation	Average:55.277; most accessible tissue: Minghui63 flag leaf, score: 66.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420836195	NA	3.27E-06	mr1030	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
vg0420836195	NA	3.75E-06	mr1118	Jap_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
vg0420836195	3.76E-06	7.30E-08	mr1311	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
vg0420836195	NA	6.08E-06	mr1412	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
vg0420836195	NA	7.92E-06	mr1502	Jap_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
vg0420836195	NA	6.56E-07	mr1568	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
vg0420836195	NA	3.60E-06	mr1596	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
vg0420836195	NA	4.22E-06	mr1621	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
vg0420836195	2.20E-07	2.19E-07	mr1674	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
vg0420836195	NA	3.36E-07	mr1763	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
vg0420836195	NA	1.31E-06	mr1768	Jap_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
vg0420836195	NA	6.93E-06	mr1858	Jap_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
vg0420836195	NA	6.95E-06	mr1859	Jap_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
vg0420836195	NA	6.18E-06	mr1872	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