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Detailed information for vg1124468452:

Variant ID: vg1124468452 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24468452
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TCCATCAAATTTCGCATGAATGGATTTGTCTGAAGATTCTAGTCAGACAAGCATGGAGTCACAGTGCTCTCAAATACAGCACGATCTTTCTGTTTATGTT[G/A]
CATGTTCTCTCTATAGTCTCCCGTTGTTAAGTAATTAACGGAAGCGAGAAAAGTAATTAAGGGAAGCCATAGTCAACTACAGGTCTGAGGGCAGATGTAC

Reverse complement sequence

GTACATCTGCCCTCAGACCTGTAGTTGACTATGGCTTCCCTTAATTACTTTTCTCGCTTCCGTTAATTACTTAACAACGGGAGACTATAGAGAGAACATG[C/T]
AACATAAACAGAAAGATCGTGCTGTATTTGAGAGCACTGTGACTCCATGCTTGTCTGACTAGAATCTTCAGACAAATCCATTCATGCGAAATTTGATGGA

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	34.40%	10.60%	0.83%	54.15%	NA
All Indica	2759	30.70%	4.80%	0.80%	63.68%	NA
All Japonica	1512	46.80%	7.70%	0.53%	45.04%	NA
Aus	269	5.60%	67.70%	0.37%	26.39%	NA
Indica I	595	29.20%	0.20%	0.17%	70.42%	NA
Indica II	465	31.60%	10.50%	0.43%	57.42%	NA
Indica III	913	26.50%	1.80%	1.53%	70.21%	NA
Indica Intermediate	786	36.30%	8.40%	0.64%	54.71%	NA
Temperate Japonica	767	48.10%	1.20%	0.39%	50.33%	NA
Tropical Japonica	504	49.20%	15.70%	0.60%	34.52%	NA
Japonica Intermediate	241	37.30%	11.60%	0.83%	50.21%	NA
VI/Aromatic	96	15.60%	63.50%	7.29%	13.54%	NA
Intermediate	90	45.60%	12.20%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124468452	G -> A	LOC_Os11g40870-LOC_Os11g40890	intergenic_region ; MODIFIER	silent_mutation	Average:45.439; most accessible tissue: Callus, score: 60.219	N	N	N	N
vg1124468452	G -> DEL	N	N	silent_mutation	Average:45.439; most accessible tissue: Callus, score: 60.219	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124468452	6.05E-17	7.24E-20	mr1238	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
vg1124468452	3.18E-16	2.40E-19	mr1309	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
vg1124468452	7.71E-08	1.43E-08	mr1484	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
vg1124468452	3.23E-06	3.23E-06	mr1566	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
vg1124468452	2.73E-11	9.32E-14	mr1841	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
vg1124468452	1.13E-11	1.13E-11	mr1900	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
vg1124468452	9.10E-06	9.10E-06	mr1945	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
vg1124468452	2.58E-15	1.32E-18	mr1238_2	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
vg1124468452	1.89E-16	1.54E-19	mr1484_2	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
vg1124468452	4.93E-07	1.97E-08	mr1609_2	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
vg1124468452	1.41E-17	1.42E-22	mr1841_2	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
vg1124468452	1.15E-11	3.83E-15	mr1900_2	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
vg1124468452	4.08E-13	4.08E-13	mr1945_2	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