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Detailed information for vg0816930005:

Variant ID: vg0816930005 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16930005
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAGTGAATAGCTTTTTCACCTCTCAGTAACCTCCTGATTAGGTTATTTATGTTGTAAAGGAGGTATCTAGCTTGTCTTAGTGGTCGTCACGTTTAGCA[G/T,A]
ATCTCGAGGGTGCCCTTGCAAATCAAGATCGTCGTATCCAATACTGGAAGACGAAATTTGAAGTGGCGGAACTTGAGAGAACCATGCTGGCCGTGAAAAA

Reverse complement sequence

TTTTTCACGGCCAGCATGGTTCTCTCAAGTTCCGCCACTTCAAATTTCGTCTTCCAGTATTGGATACGACGATCTTGATTTGCAAGGGCACCCTCGAGAT[C/A,T]
TGCTAAACGTGACGACCACTAAGACAAGCTAGATACCTCCTTTACAACATAAATAACCTAATCAGGAGGTTACTGAGAGGTGAAAAAGCTATTCACTTGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	1.20%	2.67%	11.85%	NA
All Indica	2759	89.10%	1.80%	2.28%	6.81%	NA
All Japonica	1512	73.00%	0.10%	3.70%	23.15%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	92.30%	0.30%	2.18%	5.21%	NA
Indica II	465	85.80%	1.70%	3.23%	9.25%	NA
Indica III	913	88.70%	3.10%	1.86%	6.35%	NA
Indica Intermediate	786	89.20%	1.40%	2.29%	7.12%	NA
Temperate Japonica	767	78.90%	0.00%	0.78%	20.34%	NA
Tropical Japonica	504	69.60%	0.20%	9.13%	21.03%	NA
Japonica Intermediate	241	61.40%	0.40%	1.66%	36.51%	NA
VI/Aromatic	96	79.20%	2.10%	6.25%	12.50%	NA
Intermediate	90	87.80%	2.20%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816930005	G -> T	LOC_Os08g27790.1	splice_acceptor_variant&intron_variant ; HIGH	splice_acceptor_variant	Average:33.318; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0816930005	G -> A	LOC_Os08g27790.1	splice_acceptor_variant&intron_variant ; HIGH	N	Average:33.318; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0816930005	G -> DEL	LOC_Os08g27790.1	N	splice_acceptor_variant	Average:33.318; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816930005	2.48E-06	2.37E-06	mr1717_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
vg0816930005	4.00E-06	4.00E-06	mr1770_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