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Detailed information for vg0817080710:

Variant ID: vg0817080710 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17080710
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTACGACCAACTGCATATCATGAAACTTCCCCAATGCAGTTAGTACGTGGAAATCCTCCAAGTATTTCCCATTTGCGTAAGTTCGGATGTGCTGTAT[G/A]
CATACCGATCTCACCACCACAGCGTACCGCTATGGGCCCACACAGGAAAGTGGGGATCTATGTGGGATTCAAATCTCCGTTGATCATAAAGTATTTAGAA

Reverse complement sequence

TTCTAAATACTTTATGATCAACGGAGATTTGAATCCCACATAGATCCCCACTTTCCTGTGTGGGCCCATAGCGGTACGCTGTGGTGGTGAGATCGGTATG[C/T]
ATACAGCACATCCGAACTTACGCAAATGGGAAATACTTGGAGGATTTCCACGTACTAACTGCATTGGGGAAGTTTCATGATATGCAGTTGGTCGTAGTTG

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	94.60%	5.00%	0.42%	0.00%	NA
All Indica	2759	95.90%	3.60%	0.51%	0.00%	NA
All Japonica	1512	94.80%	4.90%	0.33%	0.00%	NA
Aus	269	81.00%	18.60%	0.37%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	93.60%	6.00%	0.33%	0.00%	NA
Indica Intermediate	786	93.40%	5.20%	1.40%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	86.90%	12.30%	0.79%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817080710	G -> A	LOC_Os08g28040.1	missense_variant ; p.Cys395Tyr; MODERATE	nonsynonymous_codon ; C395Y	Average:30.068; most accessible tissue: Zhenshan97 flower, score: 37.704	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817080710	NA	5.58E-06	mr1076	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
vg0817080710	NA	3.10E-07	mr1227	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
vg0817080710	8.53E-06	6.94E-06	mr1911	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