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Detailed information for vg0611005857:

Variant ID: vg0611005857 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11005857
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CTCATGCCTTAAGATTCGTGGCATGAGACAAGAAACCGTGCGGTGGAAATTGTTTCCGTTCTCTCTTCAAGAGAGAGCAAAGCAATGGTACACCTCCACC[G/A]
TTGGATGTGTAAACGGTAGCTGGGAAAAGATGCGAGACAGATTTTGTCTTGCCTTCTTCCCAGTTACTCGTATTACTGCCCTTCGAGTAGAAATTCTCGG

Reverse complement sequence

CCGAGAATTTCTACTCGAAGGGCAGTAATACGAGTAACTGGGAAGAAGGCAAGACAAAATCTGTCTCGCATCTTTTCCCAGCTACCGTTTACACATCCAA[C/T]
GGTGGAGGTGTACCATTGCTTTGCTCTCTCTTGAAGAGAGAACGGAAACAATTTCCACCGCACGGTTTCTTGTCTCATGCCACGAATCTTAAGGCATGAG

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	90.30%	8.70%	0.30%	0.70%	NA
All Indica	2759	88.70%	9.60%	0.51%	1.20%	NA
All Japonica	1512	94.80%	5.20%	0.00%	0.00%	NA
Aus	269	78.10%	21.90%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	75.60%	20.00%	1.31%	3.07%	NA
Indica Intermediate	786	89.60%	9.50%	0.25%	0.64%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	88.10%	11.90%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0611005857	G -> A	LOC_Os06g19350.1	missense_variant ; p.Val98Ile; MODERATE	nonsynonymous_codon ; V98I	Average:39.608; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	benign	0.877	TOLERATED	0.40
vg0611005857	G -> DEL	LOC_Os06g19350.1	N	frameshift_variant	Average:39.608; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611005857	2.21E-07	1.40E-08	mr1697	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