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Detailed information for vg0914575829:

Variant ID: vg0914575829 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 14575829
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

GACTCCACAAGTTTTTCAACAAGTATTCATGGGTCTCAAGAATCCATCTGGATCAGCAACTAAATCCATTTGAAGTTAATACTATCGGGAGGTTCGAATC[A/G]
AATCCAAAATATGCAGAACTTAATCTTTTGCATTCTGTGTAGGCCAAAAGTGATGCGGTGATGTAGGAGTATACTTAAGAAATATTTTGGTTTAGTCTTC

Reverse complement sequence

GAAGACTAAACCAAAATATTTCTTAAGTATACTCCTACATCACCGCATCACTTTTGGCCTACACAGAATGCAAAAGATTAAGTTCTGCATATTTTGGATT[T/C]
GATTCGAACCTCCCGATAGTATTAACTTCAAATGGATTTAGTTGCTGATCCAGATGGATTCTTGAGACCCATGAATACTTGTTGAAAAACTTGTGGAGTC

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	96.60%	3.30%	0.06%	0.00%	NA
All Indica	2759	94.30%	5.60%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	79.70%	20.20%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.20%	1.60%	0.11%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0914575829	A -> G	LOC_Os09g24480-LOC_Os09g24490	intergenic_region ; MODIFIER	silent_mutation	Average:31.489; most accessible tissue: Zhenshan97 young leaf, score: 51.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0914575829	NA	3.97E-06	mr1045_2	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
vg0914575829	3.45E-06	5.67E-09	mr1517_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