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Detailed information for vg0619229693:

Variant ID: vg0619229693 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19229693
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TTCATTTTCCAGTGAGTACATGCATGATCCAAAATTATATTGAATTGAATCTCTAATTACAGTTAATATAAAGAGTATATTAAATCTCTCTTTGTTTCTC[G/A]
TGTAGTGTGGAAAGCAGGAACAGGGAACTAACTTATGCGGCTACTACGTATGCGAGTATGCCCACTGCCTATCAAACCAAATATGCACAACACGAGAGCT

Reverse complement sequence

AGCTCTCGTGTTGTGCATATTTGGTTTGATAGGCAGTGGGCATACTCGCATACGTAGTAGCCGCATAAGTTAGTTCCCTGTTCCTGCTTTCCACACTACA[C/T]
GAGAAACAAAGAGAGATTTAATATACTCTTTATATTAACTGTAATTAGAGATTCAATTCAATATAATTTTGGATCATGCATGTACTCACTGGAAAATGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.90%	45.80%	0.36%	5.97%	NA
All Indica	2759	76.00%	23.60%	0.04%	0.43%	NA
All Japonica	1512	2.30%	79.20%	0.93%	17.53%	NA
Aus	269	34.60%	65.10%	0.37%	0.00%	NA
Indica I	595	78.70%	19.80%	0.00%	1.51%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	70.20%	29.80%	0.00%	0.00%	NA
Indica Intermediate	786	70.40%	29.10%	0.13%	0.38%	NA
Temperate Japonica	767	3.30%	69.00%	1.04%	26.73%	NA
Tropical Japonica	504	0.80%	96.00%	0.40%	2.78%	NA
Japonica Intermediate	241	2.50%	76.80%	1.66%	19.09%	NA
VI/Aromatic	96	1.00%	97.90%	1.04%	0.00%	NA
Intermediate	90	42.20%	52.20%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619229693	G -> A	LOC_Os06g33030.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:31.197; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N
vg0619229693	G -> A	LOC_Os06g33040.1	downstream_gene_variant ; 1495.0bp to feature; MODIFIER	silent_mutation	Average:31.197; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N
vg0619229693	G -> DEL	N	N	silent_mutation	Average:31.197; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619229693	NA	1.47E-07	mr1354	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
vg0619229693	NA	3.03E-15	mr1916	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
vg0619229693	NA	2.39E-06	mr1094_2	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
vg0619229693	NA	5.62E-06	mr1291_2	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
vg0619229693	NA	4.14E-06	mr1428_2	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
vg0619229693	NA	8.46E-15	mr1454_2	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
vg0619229693	2.92E-06	2.92E-06	mr1477_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
vg0619229693	NA	9.17E-06	mr1992_2	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