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Detailed information for vg1002771978:

Variant ID: vg1002771978 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2771978
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTTATTTGGTCGCTACATAAAAATGGCCATTTTTCGGTCAAATCCATGTATAATGCGATCATCAATTCCAATGTAAGAATCCACAAGAGGATCTTATG[G/A]
GAGGTAAAGGTACCACTAAAAATCAAAGTATTTATGTGGTTTCTTCACAAAAAAAAGTAATCTTGACGAAAGATAATCTCATAAAGAGAAATTGAAGGGG

Reverse complement sequence

CCCCTTCAATTTCTCTTTATGAGATTATCTTTCGTCAAGATTACTTTTTTTTGTGAAGAAACCACATAAATACTTTGATTTTTAGTGGTACCTTTACCTC[C/T]
CATAAGATCCTCTTGTGGATTCTTACATTGGAATTGATGATCGCATTATACATGGATTTGACCGAAAAATGGCCATTTTTATGTAGCGACCAAATAAAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.70%	17.30%	2.05%	0.00%	NA
All Indica	2759	94.80%	2.40%	2.86%	0.00%	NA
All Japonica	1512	59.90%	39.80%	0.26%	0.00%	NA
Aus	269	45.70%	50.20%	4.09%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	88.90%	3.00%	8.11%	0.00%	NA
Indica Intermediate	786	95.80%	3.70%	0.51%	0.00%	NA
Temperate Japonica	767	87.70%	12.10%	0.13%	0.00%	NA
Tropical Japonica	504	14.70%	84.90%	0.40%	0.00%	NA
Japonica Intermediate	241	66.00%	33.60%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	81.10%	16.70%	2.22%	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
vg1002771978	G -> A	LOC_Os10g05580.1	upstream_gene_variant ; 1057.0bp to feature; MODIFIER	silent_mutation	Average:12.295; most accessible tissue: Callus, score: 24.775	N	N	N	N
vg1002771978	G -> A	LOC_Os10g05570-LOC_Os10g05580	intergenic_region ; MODIFIER	silent_mutation	Average:12.295; most accessible tissue: Callus, score: 24.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002771978	NA	3.79E-06	mr1156	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
vg1002771978	NA	5.79E-06	mr1179	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
vg1002771978	NA	8.51E-06	mr1220	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
vg1002771978	3.71E-07	1.89E-12	mr1248	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
vg1002771978	NA	5.06E-09	mr1248	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
vg1002771978	NA	9.46E-08	mr1338	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
vg1002771978	NA	4.24E-06	mr1425	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
vg1002771978	NA	1.54E-06	mr1736	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
vg1002771978	NA	5.76E-07	mr1742	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
vg1002771978	3.70E-06	8.20E-10	mr1746	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
vg1002771978	NA	1.62E-08	mr1951	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
vg1002771978	NA	7.30E-06	mr1991	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