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Detailed information for vg0816926894:

Variant ID: vg0816926894 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16926894
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTCTCGACGACTTGGCTCCTCGCAGACTTCGGCTTTGTAGGCTGTGTGGGTTGTGTTGGCTCTGAGATTCGATGATCCATGCCCTCCCCGGGGGGTCC[C/G]
TTTTATATCATAGATCTGGAGGTTTTCAAGTAGGACTCAGAGATATCAGACCCAATACGATACGTCGACGACCCAGTTCTGTCCGAGAAGGACTCTTCCC

Reverse complement sequence

GGGAAGAGTCCTTCTCGGACAGAACTGGGTCGTCGACGTATCGTATTGGGTCTGATATCTCTGAGTCCTACTTGAAAACCTCCAGATCTATGATATAAAA[G/C]
GGACCCCCCGGGGAGGGCATGGATCATCGAATCTCAGAGCCAACACAACCCACACAGCCTACAAAGCCGAAGTCTGCGAGGAGCCAAGTCGTCGAGAGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.70%	14.00%	4.42%	47.86%	NA
All Indica	2759	19.60%	20.60%	2.57%	57.23%	NA
All Japonica	1512	53.20%	5.30%	5.75%	35.71%	NA
Aus	269	79.20%	0.00%	4.83%	15.99%	NA
Indica I	595	33.30%	38.80%	0.34%	27.56%	NA
Indica II	465	10.10%	5.80%	6.24%	77.85%	NA
Indica III	913	18.10%	15.90%	2.08%	63.96%	NA
Indica Intermediate	786	16.50%	21.10%	2.67%	59.67%	NA
Temperate Japonica	767	73.50%	0.10%	3.26%	23.08%	NA
Tropical Japonica	504	24.20%	14.90%	10.91%	50.00%	NA
Japonica Intermediate	241	49.40%	1.70%	2.90%	46.06%	NA
VI/Aromatic	96	7.30%	1.00%	27.08%	64.58%	NA
Intermediate	90	32.20%	12.20%	13.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816926894	C -> G	LOC_Os08g27790.1	upstream_gene_variant ; 619.0bp to feature; MODIFIER	silent_mutation	Average:31.833; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0816926894	C -> G	LOC_Os08g27800.1	downstream_gene_variant ; 4728.0bp to feature; MODIFIER	silent_mutation	Average:31.833; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0816926894	C -> G	LOC_Os08g27780-LOC_Os08g27790	intergenic_region ; MODIFIER	silent_mutation	Average:31.833; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0816926894	C -> DEL	N	N	silent_mutation	Average:31.833; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816926894	3.58E-06	3.58E-06	mr1591	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