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Detailed information for vg0709590699:

Variant ID: vg0709590699 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9590699
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CACAACAGTAGCTCGCGAACTGGTCATTAATTGCCATGAGCACGACCTTCAAAACCATGTGCTCACAACCCACCATTAATCATATTTTAGTTACCAATTA[G/A]
TTATCATAACACGATTAACCATCGTGAGCTACCATTAAATATAACCATAAATAATAATGTAATATATATGATTCATCCCATTAGTGAGCTAATGTTTCTA

Reverse complement sequence

TAGAAACATTAGCTCACTAATGGGATGAATCATATATATTACATTATTATTTATGGTTATATTTAATGGTAGCTCACGATGGTTAATCGTGTTATGATAA[C/T]
TAATTGGTAACTAAAATATGATTAATGGTGGGTTGTGAGCACATGGTTTTGAAGGTCGTGCTCATGGCAATTAATGACCAGTTCGCGAGCTACTGTTGTG

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	31.40%	1.50%	20.12%	46.93%	NA
All Indica	2759	6.80%	2.40%	26.39%	64.44%	NA
All Japonica	1512	68.00%	0.10%	7.54%	24.40%	NA
Aus	269	68.00%	1.50%	18.96%	11.52%	NA
Indica I	595	7.10%	1.00%	35.80%	56.13%	NA
Indica II	465	6.00%	0.90%	18.92%	74.19%	NA
Indica III	913	1.40%	4.70%	24.53%	69.33%	NA
Indica Intermediate	786	13.20%	1.70%	25.83%	59.29%	NA
Temperate Japonica	767	60.10%	0.10%	2.87%	36.90%	NA
Tropical Japonica	504	86.90%	0.00%	11.71%	1.39%	NA
Japonica Intermediate	241	53.50%	0.00%	13.69%	32.78%	NA
VI/Aromatic	96	49.00%	0.00%	40.62%	10.42%	NA
Intermediate	90	45.60%	0.00%	21.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709590699	G -> DEL	N	N	silent_mutation	Average:48.381; most accessible tissue: Minghui63 young leaf, score: 75.006	N	N	N	N
vg0709590699	G -> A	LOC_Os07g16400.1	intron_variant ; MODIFIER	silent_mutation	Average:48.381; most accessible tissue: Minghui63 young leaf, score: 75.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709590699	NA	1.13E-15	mr1270	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
vg0709590699	NA	2.45E-06	mr1398	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
vg0709590699	NA	3.70E-09	mr1578	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
vg0709590699	NA	5.65E-07	mr1717	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
vg0709590699	4.99E-07	4.99E-07	mr1953	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
vg0709590699	NA	8.01E-30	mr1580_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
vg0709590699	NA	9.97E-10	mr1751_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
vg0709590699	NA	2.11E-30	mr1825_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