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Detailed information for vg0808441335:

Variant ID: vg0808441335 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8441335
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATTGATTTAAGATGTTCCAGTTTTCTTTATGATATGTTAAAAATATTATCATTGACACTATGATATGACATTCACTGCTACGGGATGGGTTTTTCCGT[G/A]
CGGTCAAAAAAAATATCCACGTGCGGATGAATGGCCCGCACGCAACACTTCGTCTGCGAAAGTCATGATTTTTGCGTGCGGGTGGCCCTCCCACACGCGA

Reverse complement sequence

TCGCGTGTGGGAGGGCCACCCGCACGCAAAAATCATGACTTTCGCAGACGAAGTGTTGCGTGCGGGCCATTCATCCGCACGTGGATATTTTTTTTGACCG[C/T]
ACGGAAAAACCCATCCCGTAGCAGTGAATGTCATATCATAGTGTCAATGATAATATTTTTAACATATCATAAAGAAAACTGGAACATCTTAAATCAATGG

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	70.40%	23.80%	2.16%	3.62%	NA
All Indica	2759	62.20%	32.30%	2.94%	2.61%	NA
All Japonica	1512	83.00%	9.60%	1.32%	6.08%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	65.20%	27.40%	3.87%	3.53%	NA
Indica II	465	74.60%	13.30%	7.96%	4.09%	NA
Indica III	913	50.80%	48.70%	0.44%	0.00%	NA
Indica Intermediate	786	65.80%	28.00%	2.16%	4.07%	NA
Temperate Japonica	767	88.30%	0.90%	1.69%	9.13%	NA
Tropical Japonica	504	76.20%	18.50%	1.19%	4.17%	NA
Japonica Intermediate	241	80.50%	18.70%	0.41%	0.41%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	66.70%	24.40%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808441335	G -> A	LOC_Os08g14109.1	intron_variant ; MODIFIER	silent_mutation	Average:40.544; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0808441335	G -> DEL	N	N	silent_mutation	Average:40.544; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808441335	1.06E-06	3.44E-06	mr1097_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
vg0808441335	NA	5.96E-06	mr1102_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
vg0808441335	NA	1.01E-06	mr1888_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