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Detailed information for vg0128212865:

Variant ID: vg0128212865 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28212865
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTGGAGAGTTTGTTCCCACTTTTTTGTGGTTTTGTTCCAAGTTAATCTAGAGAGTTTGTTTCATTGTTATTGTTTACTAAAATTATTTAGTTACCACG[G/A]
CTGATATGCTTACCGACCTTATGGAGATCGCATCTCACTATGAGCAGCTTTTGTGAGAGAGAGAGACAGAGAAAAAAGGAGTAGATCGACCAAGATGATC

Reverse complement sequence

GATCATCTTGGTCGATCTACTCCTTTTTTCTCTGTCTCTCTCTCTCACAAAAGCTGCTCATAGTGAGATGCGATCTCCATAAGGTCGGTAAGCATATCAG[C/T]
CGTGGTAACTAAATAATTTTAGTAAACAATAACAATGAAACAAACTCTCTAGATTAACTTGGAACAAAACCACAAAAAAGTGGGAACAAACTCTCCAACG

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	70.30%	29.70%	0.04%	0.00%	NA
All Indica	2759	99.10%	0.80%	0.04%	0.00%	NA
All Japonica	1512	11.90%	88.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.13%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	31.90%	68.10%	0.00%	0.00%	NA
Japonica Intermediate	241	6.20%	93.80%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	58.90%	40.00%	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
vg0128212865	G -> A	LOC_Os01g49080.1	downstream_gene_variant ; 1911.0bp to feature; MODIFIER	silent_mutation	Average:23.975; most accessible tissue: Callus, score: 43.589	N	N	N	N
vg0128212865	G -> A	LOC_Os01g49080-LOC_Os01g49090	intergenic_region ; MODIFIER	silent_mutation	Average:23.975; most accessible tissue: Callus, score: 43.589	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128212865	NA	3.36E-06	mr1277	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
vg0128212865	NA	2.80E-87	mr1334	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
vg0128212865	NA	8.98E-27	mr1423	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
vg0128212865	NA	3.16E-36	mr1486	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
vg0128212865	NA	8.34E-06	mr1596	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
vg0128212865	9.03E-07	7.31E-30	mr1805	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
vg0128212865	NA	1.54E-08	mr1805	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
vg0128212865	NA	3.15E-16	mr1277_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
vg0128212865	NA	1.95E-07	mr1277_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
vg0128212865	NA	1.40E-99	mr1334_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
vg0128212865	NA	2.18E-45	mr1486_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
vg0128212865	NA	4.37E-49	mr1805_2	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
vg0128212865	NA	6.75E-08	mr1805_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
vg0128212865	NA	7.68E-56	mr1991_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