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Detailed information for vg0803869823:

Variant ID: vg0803869823 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3869823
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCTCTAAACATGATACCCCCGGGCCCATATCACCGACATCGTCAATCTCCAGGATTTACCGGCCCAGTCTTCGAAGATGCTTATAGGTGTGTGTTATG[G/A]
GTGTCTGCGTTGTACCGTGTAATTAAAAAAGTTAATATCTGTGGGAATATGGTGTTGATCAACACATGGGAATATGTACTACTATTACGATTCCAAAATT

Reverse complement sequence

AATTTTGGAATCGTAATAGTAGTACATATTCCCATGTGTTGATCAACACCATATTCCCACAGATATTAACTTTTTTAATTACACGGTACAACGCAGACAC[C/T]
CATAACACACACCTATAAGCATCTTCGAAGACTGGGCCGGTAAATCCTGGAGATTGACGATGTCGGTGATATGGGCCCGGGGGTATCATGTTTAGAGGGA

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	65.50%	1.30%	0.25%	32.97%	NA
All Indica	2759	80.00%	2.10%	0.29%	17.62%	NA
All Japonica	1512	34.10%	0.10%	0.26%	65.61%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	90.90%	0.00%	0.34%	8.74%	NA
Indica II	465	32.00%	4.30%	0.00%	63.66%	NA
Indica III	913	96.30%	3.20%	0.22%	0.33%	NA
Indica Intermediate	786	81.20%	1.10%	0.51%	17.18%	NA
Temperate Japonica	767	48.00%	0.00%	0.26%	51.76%	NA
Tropical Japonica	504	18.30%	0.00%	0.20%	81.55%	NA
Japonica Intermediate	241	22.80%	0.40%	0.41%	76.35%	NA
VI/Aromatic	96	47.90%	0.00%	0.00%	52.08%	NA
Intermediate	90	66.70%	0.00%	0.00%	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
vg0803869823	G -> A	LOC_Os08g06940.1	downstream_gene_variant ; 3882.0bp to feature; MODIFIER	silent_mutation	Average:56.559; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0803869823	G -> A	LOC_Os08g06940-LOC_Os08g06960	intergenic_region ; MODIFIER	silent_mutation	Average:56.559; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N
vg0803869823	G -> DEL	N	N	silent_mutation	Average:56.559; most accessible tissue: Zhenshan97 flag leaf, score: 85.514	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803869823	NA	2.22E-11	mr1002	Jap_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
vg0803869823	NA	2.35E-08	mr1182	Jap_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
vg0803869823	NA	3.18E-06	mr1282	Jap_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
vg0803869823	NA	7.96E-08	mr1650	Jap_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
vg0803869823	NA	1.08E-06	mr1658	Jap_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
vg0803869823	NA	3.66E-10	mr1002_2	Jap_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
vg0803869823	NA	4.67E-08	mr1010_2	Jap_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
vg0803869823	NA	4.80E-06	mr1406_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
vg0803869823	NA	1.84E-06	mr1449_2	Jap_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