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Detailed information for vg1004591319:

Variant ID: vg1004591319 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4591319
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTCTAATCATATCTTATTTGTAGAAAGTTTTCTGAAGAGAAGCATGCAATGCATAATAATCTTTCAGTCGAGGGGCTTGATCAATTGATGAGAGAG[G/A]
AATTTGTTGACTGGTTTAAGAATGCTGTAAAAACTCTATATATATCCTTATATTTTCTTACCTATAATGTTCAAAATATATATTTTTAATTTCTAAATTA

Reverse complement sequence

TAATTTAGAAATTAAAAATATATATTTTGAACATTATAGGTAAGAAAATATAAGGATATATATAGAGTTTTTACAGCATTCTTAAACCAGTCAACAAATT[C/T]
CTCTCTCATCAATTGATCAAGCCCCTCGACTGAAAGATTATTATGCATTGCATGCTTCTCTTCAGAAAACTTTCTACAAATAAGATATGATTAGAAATTT

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	89.40%	5.40%	2.14%	3.09%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	70.60%	14.10%	6.28%	9.06%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	86.40%	5.20%	8.34%	0.00%	NA
Tropical Japonica	504	42.50%	26.00%	5.95%	25.60%	NA
Japonica Intermediate	241	78.80%	17.40%	0.41%	3.32%	NA
VI/Aromatic	96	75.00%	13.50%	5.21%	6.25%	NA
Intermediate	90	85.60%	10.00%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004591319	G -> A	LOC_Os10g08450.1	missense_variant ; p.Glu756Lys; MODERATE	nonsynonymous_codon ; E756K	Average:43.741; most accessible tissue: Callus, score: 68.581	unknown	unknown	TOLERATED	0.59
vg1004591319	G -> DEL	LOC_Os10g08450.1	N	frameshift_variant	Average:43.741; most accessible tissue: Callus, score: 68.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004591319	NA	8.64E-07	mr1420	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
vg1004591319	NA	2.85E-06	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
vg1004591319	NA	1.26E-07	mr1471	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
vg1004591319	2.81E-06	NA	mr1477	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
vg1004591319	NA	9.84E-10	mr1642	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
vg1004591319	NA	2.33E-06	mr1642	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
vg1004591319	NA	8.22E-06	mr1725	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
vg1004591319	NA	1.10E-07	mr1779	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
vg1004591319	NA	3.21E-07	mr1797	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
vg1004591319	NA	3.21E-07	mr1801	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
vg1004591319	4.45E-08	NA	mr1019_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
vg1004591319	NA	2.99E-12	mr1019_2	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
vg1004591319	5.81E-06	NA	mr1055_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
vg1004591319	NA	5.30E-11	mr1055_2	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
vg1004591319	1.62E-06	NA	mr1132_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
vg1004591319	NA	1.92E-13	mr1132_2	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
vg1004591319	8.19E-09	NA	mr1261_2	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
vg1004591319	NA	4.79E-09	mr1261_2	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
vg1004591319	NA	7.59E-06	mr1415_2	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
vg1004591319	NA	1.81E-06	mr1632_2	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