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Detailed information for vg0705226228:

Variant ID: vg0705226228 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5226228
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAGTAATTCATCATCCTGTGGTTTGACATGATAATTTTGCATTATTGGTAATAAAAGATAATATTTGTCCCCAAAAGGCCTTACTGTGGGCAACTCTA[G/A]
AACCTTTTCCATAGTATCATAGCCATGACCATGAGTTTTTATGTACTCCATGGTCCACCATGCTTATATTTATCTTTGGTTTTTACTGTCTGTTTCCTTT

Reverse complement sequence

AAAGGAAACAGACAGTAAAAACCAAAGATAAATATAAGCATGGTGGACCATGGAGTACATAAAAACTCATGGTCATGGCTATGATACTATGGAAAAGGTT[C/T]
TAGAGTTGCCCACAGTAAGGCCTTTTGGGGACAAATATTATCTTTTATTACCAATAATGCAAAATTATCATGTCAAACCACAGGATGATGAATTACTTGA

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	51.50%	48.40%	0.15%	0.00%	NA
All Indica	2759	84.30%	15.40%	0.25%	0.00%	NA
All Japonica	1512	0.30%	99.70%	0.00%	0.00%	NA
Aus	269	24.20%	75.80%	0.00%	0.00%	NA
Indica I	595	93.80%	6.10%	0.17%	0.00%	NA
Indica II	465	90.10%	9.20%	0.65%	0.00%	NA
Indica III	913	76.50%	23.40%	0.11%	0.00%	NA
Indica Intermediate	786	82.80%	16.90%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0705226228	G -> A	LOC_Os07g09830.1	downstream_gene_variant ; 2628.0bp to feature; MODIFIER	silent_mutation	Average:47.113; most accessible tissue: Callus, score: 91.902	N	N	N	N
vg0705226228	G -> A	LOC_Os07g09814.3	downstream_gene_variant ; 2447.0bp to feature; MODIFIER	silent_mutation	Average:47.113; most accessible tissue: Callus, score: 91.902	N	N	N	N
vg0705226228	G -> A	LOC_Os07g09814.1	intron_variant ; MODIFIER	silent_mutation	Average:47.113; most accessible tissue: Callus, score: 91.902	N	N	N	N
vg0705226228	G -> A	LOC_Os07g09814.2	intron_variant ; MODIFIER	silent_mutation	Average:47.113; most accessible tissue: Callus, score: 91.902	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705226228	NA	3.61E-32	mr1026	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
vg0705226228	NA	2.41E-10	mr1151	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
vg0705226228	NA	9.62E-07	mr1152	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
vg0705226228	NA	1.17E-32	mr1213	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
vg0705226228	NA	1.38E-14	mr1261	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
vg0705226228	NA	8.98E-14	mr1531	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
vg0705226228	NA	1.31E-08	mr1707	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
vg0705226228	NA	8.05E-06	mr1707	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
vg0705226228	NA	3.05E-15	mr1744	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
vg0705226228	NA	1.03E-15	mr1744_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
vg0705226228	NA	3.86E-07	mr1834_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