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Detailed information for vg0809931541:

Variant ID: vg0809931541 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9931541
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTACTGGTACCGTGAAAGAGAGGGATAAATCAGGGTGCATTCACCGCCGGGTGCTCATCACTACTCCTAATTGTAACTAGACCTAATCATATGACTT[C/A]
CCTACACTACTTATCATCTGACTCCAACCGTACTTGAGAGTGGAAGAATTATAGCCTAATCATCTCTTTAATCATCCAACTATTACACTAATCAGAATTA

Reverse complement sequence

TAATTCTGATTAGTGTAATAGTTGGATGATTAAAGAGATGATTAGGCTATAATTCTTCCACTCTCAAGTACGGTTGGAGTCAGATGATAAGTAGTGTAGG[G/T]
AAGTCATATGATTAGGTCTAGTTACAATTAGGAGTAGTGATGAGCACCCGGCGGTGAATGCACCCTGATTTATCCCTCTCTTTCACGGTACCAGTAATTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.30%	9.40%	0.61%	43.65%	NA
All Indica	2759	32.80%	0.20%	0.69%	66.29%	NA
All Japonica	1512	66.70%	28.00%	0.33%	4.89%	NA
Aus	269	49.10%	0.00%	1.12%	49.81%	NA
Indica I	595	18.80%	0.00%	0.67%	80.50%	NA
Indica II	465	53.80%	0.40%	0.43%	45.38%	NA
Indica III	913	32.60%	0.20%	0.99%	66.16%	NA
Indica Intermediate	786	31.30%	0.10%	0.51%	68.07%	NA
Temperate Japonica	767	94.10%	2.20%	0.13%	3.52%	NA
Tropical Japonica	504	37.70%	57.10%	0.40%	4.76%	NA
Japonica Intermediate	241	40.20%	49.40%	0.83%	9.54%	NA
VI/Aromatic	96	93.80%	2.10%	0.00%	4.17%	NA
Intermediate	90	58.90%	14.40%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809931541	C -> A	LOC_Os08g16270.1	downstream_gene_variant ; 717.0bp to feature; MODIFIER	silent_mutation	Average:46.354; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0809931541	C -> A	LOC_Os08g16280.1	downstream_gene_variant ; 4830.0bp to feature; MODIFIER	silent_mutation	Average:46.354; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0809931541	C -> A	LOC_Os08g16260-LOC_Os08g16270	intergenic_region ; MODIFIER	silent_mutation	Average:46.354; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0809931541	C -> DEL	N	N	silent_mutation	Average:46.354; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809931541	6.16E-06	NA	mr1095	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
vg0809931541	NA	4.95E-07	mr1906	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
vg0809931541	NA	5.19E-06	mr1960	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