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Detailed information for vg0709331066:

Variant ID: vg0709331066 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9331066
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.32, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

CCAAGTGGCTTCATCCTCAGTGTGATTACTCCACTGTACCTTATACATACGCCATACTTTGTTCCTAGTCCTCTTTTCTGCTTCATCCAATATCCGGACT[A/G]
GGTGTTCTGGATACGTGAGATCATTGCTAATGTGAATTTCTTCCAACGGAGCTTGTTCTTCCGGCACTCGTAAGCATTTCTTTAATTGAGACACATGGAA

Reverse complement sequence

TTCCATGTGTCTCAATTAAAGAAATGCTTACGAGTGCCGGAAGAACAAGCTCCGTTGGAAGAAATTCACATTAGCAATGATCTCACGTATCCAGAACACC[T/C]
AGTCCGGATATTGGATGAAGCAGAAAAGAGGACTAGGAACAAAGTATGGCGTATGTATAAGGTACAGTGGAGTAATCACACTGAGGATGAAGCCACTTGG

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	39.10%	0.20%	1.61%	59.08%	NA
All Indica	2759	5.50%	0.30%	2.68%	91.48%	NA
All Japonica	1512	94.70%	0.00%	0.13%	5.16%	NA
Aus	269	65.40%	0.00%	0.00%	34.57%	NA
Indica I	595	7.20%	0.00%	1.85%	90.92%	NA
Indica II	465	7.50%	0.00%	2.15%	90.32%	NA
Indica III	913	2.00%	0.90%	3.29%	93.87%	NA
Indica Intermediate	786	7.10%	0.10%	2.93%	89.82%	NA
Temperate Japonica	767	97.90%	0.00%	0.13%	1.96%	NA
Tropical Japonica	504	88.50%	0.00%	0.20%	11.31%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	49.00%	0.00%	0.00%	51.04%	NA
Intermediate	90	46.70%	0.00%	0.00%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709331066	A -> DEL	LOC_Os07g16010.1	N	frameshift_variant	Average:14.047; most accessible tissue: Callus, score: 17.287	N	N	N	N
vg0709331066	A -> G	LOC_Os07g16010.1	missense_variant ; p.Leu158Pro; MODERATE	nonsynonymous_codon ; L158P	Average:14.047; most accessible tissue: Callus, score: 17.287	benign	-0.005	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709331066	NA	1.56E-21	mr1051	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
vg0709331066	NA	1.50E-18	mr1179	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
vg0709331066	NA	3.76E-10	mr1195	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
vg0709331066	9.54E-07	NA	mr1203	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
vg0709331066	NA	3.36E-31	mr1225	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
vg0709331066	NA	3.13E-10	mr1299	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
vg0709331066	NA	3.17E-10	mr1316	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
vg0709331066	5.97E-06	NA	mr1395	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
vg0709331066	9.63E-07	NA	mr1618	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
vg0709331066	NA	1.88E-20	mr1689	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
vg0709331066	NA	1.93E-16	mr1700	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
vg0709331066	NA	1.12E-06	mr1756	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
vg0709331066	NA	1.20E-07	mr1335_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