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Detailed information for vg0817612440:

Variant ID: vg0817612440 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17612440
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAAGGAAGAGAGGATGGGATAAAAAAATCTGTAAAGGTGAGTGTTATTTTTGTATGCAGTCCACTTAAGAGGCTCGCCTGCGAAATATGCTTATTTTT[G/A]
CGTGTGGTCCATATAAGAGGCCCGTAAGTGAAAATCTATTTTTCAATGCGATCCTCTTAAGGAGCCGCACACGAAAATGGAGGACAATTTTTGCAGACGC

Reverse complement sequence

GCGTCTGCAAAAATTGTCCTCCATTTTCGTGTGCGGCTCCTTAAGAGGATCGCATTGAAAAATAGATTTTCACTTACGGGCCTCTTATATGGACCACACG[C/T]
AAAAATAAGCATATTTCGCAGGCGAGCCTCTTAAGTGGACTGCATACAAAAATAACACTCACCTTTACAGATTTTTTTATCCCATCCTCTCTTCCTTTCC

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	59.70%	40.20%	0.06%	0.00%	NA
All Indica	2759	88.50%	11.50%	0.04%	0.00%	NA
All Japonica	1512	17.40%	82.50%	0.07%	0.00%	NA
Aus	269	27.90%	72.10%	0.00%	0.00%	NA
Indica I	595	95.10%	4.90%	0.00%	0.00%	NA
Indica II	465	92.00%	8.00%	0.00%	0.00%	NA
Indica III	913	81.90%	18.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.90%	10.90%	0.13%	0.00%	NA
Temperate Japonica	767	2.30%	97.70%	0.00%	0.00%	NA
Tropical Japonica	504	39.70%	60.10%	0.20%	0.00%	NA
Japonica Intermediate	241	18.70%	81.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	96.90%	1.04%	0.00%	NA
Intermediate	90	45.60%	54.40%	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
vg0817612440	G -> A	LOC_Os08g28790.1	upstream_gene_variant ; 1131.0bp to feature; MODIFIER	silent_mutation	Average:68.681; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg0817612440	G -> A	LOC_Os08g28784-LOC_Os08g28790	intergenic_region ; MODIFIER	silent_mutation	Average:68.681; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817612440	8.80E-07	9.72E-14	mr1040	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
vg0817612440	NA	2.70E-06	mr1040	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
vg0817612440	3.19E-06	2.35E-18	mr1362	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
vg0817612440	NA	1.13E-08	mr1533	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
vg0817612440	NA	1.94E-10	mr1581	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
vg0817612440	1.15E-10	3.00E-16	mr1836	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
vg0817612440	NA	1.49E-06	mr1836	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
vg0817612440	NA	8.68E-11	mr1980	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
vg0817612440	8.66E-10	1.41E-22	mr1040_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
vg0817612440	2.89E-10	1.93E-27	mr1362_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
vg0817612440	NA	1.73E-06	mr1362_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
vg0817612440	NA	4.10E-11	mr1533_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
vg0817612440	4.12E-11	1.77E-25	mr1836_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
vg0817612440	NA	6.12E-06	mr1836_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
vg0817612440	NA	1.07E-07	mr1885_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