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Detailed information for vg0603483061:

Variant ID: vg0603483061 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3483061
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTCTTTTAGCTAATCATGGCATCAAGCTATCAACATGGTCCGAATATTTAATATTTGAACTATAAATTAAATTAGTAATTAACCTTCCCTTTGTTTGG[G/A]
TTTGCTTTCTTTGTAATTATTTACGGTTTGGCAAGCAATAGCAATCATAACAACCAGCATGATGCAAAAGTTTTAAAAAGTTCAAAATTTTAGTGATTTT

Reverse complement sequence

AAAATCACTAAAATTTTGAACTTTTTAAAACTTTTGCATCATGCTGGTTGTTATGATTGCTATTGCTTGCCAAACCGTAAATAATTACAAAGAAAGCAAA[C/T]
CCAAACAAAGGGAAGGTTAATTACTAATTTAATTTATAGTTCAAATATTAAATATTCGGACCATGTTGATAGCTTGATGCCATGATTAGCTAAAAGAAAC

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	55.80%	9.80%	19.61%	14.81%	NA
All Indica	2759	76.70%	0.70%	13.37%	9.21%	NA
All Japonica	1512	7.70%	28.50%	35.32%	28.51%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	70.90%	1.00%	20.67%	7.39%	NA
Indica II	465	78.90%	0.60%	11.83%	8.60%	NA
Indica III	913	77.90%	0.20%	10.95%	10.95%	NA
Indica Intermediate	786	78.40%	1.10%	11.58%	8.91%	NA
Temperate Japonica	767	3.00%	52.70%	8.47%	35.85%	NA
Tropical Japonica	504	12.50%	2.00%	72.62%	12.90%	NA
Japonica Intermediate	241	12.40%	7.10%	42.74%	37.76%	NA
VI/Aromatic	96	86.50%	6.20%	7.29%	0.00%	NA
Intermediate	90	60.00%	4.40%	18.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0603483061	G -> A	LOC_Os06g07270.1	downstream_gene_variant ; 564.0bp to feature; MODIFIER	silent_mutation	Average:22.144; most accessible tissue: Callus, score: 41.206	N	N	N	N
vg0603483061	G -> A	LOC_Os06g07260-LOC_Os06g07270	intergenic_region ; MODIFIER	silent_mutation	Average:22.144; most accessible tissue: Callus, score: 41.206	N	N	N	N
vg0603483061	G -> DEL	N	N	silent_mutation	Average:22.144; most accessible tissue: Callus, score: 41.206	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603483061	NA	5.45E-19	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603483061	NA	8.20E-11	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603483061	1.47E-07	4.39E-15	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603483061	NA	2.52E-12	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603483061	2.01E-08	NA	Plant_height	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603483061	NA	1.23E-08	mr1549	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
vg0603483061	NA	3.61E-08	mr1624	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
vg0603483061	NA	9.44E-06	mr1346_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
vg0603483061	NA	1.06E-06	mr1354_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
vg0603483061	NA	1.88E-07	mr1482_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
vg0603483061	NA	1.54E-10	mr1624_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
vg0603483061	NA	1.16E-06	mr1693_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
vg0603483061	NA	1.78E-06	mr1723_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
vg0603483061	NA	8.04E-09	mr1741_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
vg0603483061	NA	6.55E-06	mr1757_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