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Detailed information for vg0605865870:

Variant ID: vg0605865870 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5865870
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CAATGTGATTGCTTTCACCAAGAAAACCATAAGAGCTGATACCAAAAACCCACAATGGCCTTGTGAACTCAGCATCTAGCGTGTAAACTGAAATAACCTC[G/A]
TTGGTGTGCTCAACCTGATGACAAACAAGTGCATTGGCAATGTATGTCAAACAAAATCCAGATGATGACCAAGAATGCTGTATTTGATCATGCAATGAGC

Reverse complement sequence

GCTCATTGCATGATCAAATACAGCATTCTTGGTCATCATCTGGATTTTGTTTGACATACATTGCCAATGCACTTGTTTGTCATCAGGTTGAGCACACCAA[C/T]
GAGGTTATTTCAGTTTACACGCTAGATGCTGAGTTCACAAGGCCATTGTGGGTTTTTGGTATCAGCTCTTATGGTTTTCTTGGTGAAAGCAATCACATTG

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	65.70%	34.00%	0.08%	0.15%	NA
All Indica	2759	65.60%	34.10%	0.04%	0.25%	NA
All Japonica	1512	75.80%	24.10%	0.07%	0.00%	NA
Aus	269	5.90%	94.10%	0.00%	0.00%	NA
Indica I	595	91.10%	8.90%	0.00%	0.00%	NA
Indica II	465	41.50%	57.80%	0.00%	0.65%	NA
Indica III	913	60.70%	39.10%	0.11%	0.11%	NA
Indica Intermediate	786	66.40%	33.20%	0.00%	0.38%	NA
Temperate Japonica	767	98.60%	1.30%	0.13%	0.00%	NA
Tropical Japonica	504	42.50%	57.50%	0.00%	0.00%	NA
Japonica Intermediate	241	73.00%	27.00%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	13.50%	1.04%	0.00%	NA
Intermediate	90	56.70%	42.20%	1.11%	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
vg0605865870	G -> A	LOC_Os06g11180.1	synonymous_variant ; p.Asn289Asn; LOW	synonymous_codon	Average:33.042; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg0605865870	G -> DEL	LOC_Os06g11180.1	N	frameshift_variant	Average:33.042; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605865870	NA	6.89E-06	mr1308	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
vg0605865870	NA	4.86E-08	mr1530	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
vg0605865870	1.01E-06	1.01E-06	mr1581_2	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
vg0605865870	NA	3.06E-06	mr1819_2	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
vg0605865870	NA	7.44E-06	mr1851_2	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
vg0605865870	NA	1.93E-09	mr1864_2	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
vg0605865870	NA	6.36E-08	mr1952_2	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