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Detailed information for vg0709859067:

Variant ID: vg0709859067 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9859067
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGAGGCCACATGCTGCCATCTTATCCTTCTCTGTGACAGAAGAGACATTCAGATTGGTCAGGTCACCGCCCTTTCAGGTTTCAGGAGTGCACTTGGTG[G/A]
ATCTCTCTGGTAACCTGTGCATGGTCCGGGACCTTCGTCGCATGTCGTCTACGCTGGAGATTTGGAAGCTGAATGATCTTTACTCCAGTGATTGGTCATT

Reverse complement sequence

AATGACCAATCACTGGAGTAAAGATCATTCAGCTTCCAAATCTCCAGCGTAGACGACATGCGACGAAGGTCCCGGACCATGCACAGGTTACCAGAGAGAT[C/T]
CACCAAGTGCACTCCTGAAACCTGAAAGGGCGGTGACCTGACCAATCTGAATGTCTCTTCTGTCACAGAGAAGGATAAGATGGCAGCATGTGGCCTCAAG

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	52.80%	38.60%	0.85%	7.79%	NA
All Indica	2759	83.80%	15.80%	0.14%	0.29%	NA
All Japonica	1512	2.60%	75.10%	1.52%	20.77%	NA
Aus	269	32.30%	64.30%	1.49%	1.86%	NA
Indica I	595	62.90%	37.10%	0.00%	0.00%	NA
Indica II	465	89.50%	9.90%	0.43%	0.22%	NA
Indica III	913	96.10%	3.50%	0.00%	0.44%	NA
Indica Intermediate	786	82.10%	17.30%	0.25%	0.38%	NA
Temperate Japonica	767	3.70%	72.10%	1.30%	22.95%	NA
Tropical Japonica	504	0.80%	93.80%	0.20%	5.16%	NA
Japonica Intermediate	241	2.90%	45.60%	4.98%	46.47%	NA
VI/Aromatic	96	17.70%	38.50%	9.38%	34.38%	NA
Intermediate	90	43.30%	47.80%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709859067	G -> DEL	LOC_Os07g16800.1	N	frameshift_variant	Average:16.354; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0709859067	G -> A	LOC_Os07g16800.1	missense_variant ; p.Asp286Asn; MODERATE	nonsynonymous_codon ; D286N	Average:16.354; most accessible tissue: Minghui63 panicle, score: 34.226	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709859067	4.15E-06	9.68E-23	mr1689	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