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Detailed information for vg1127460166:

Variant ID: vg1127460166 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27460166
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.28, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCAGGCAGAACGACCCTGACCAAGTTAGTCCTTACGGTGCAATCCATCTACCTCTTGAGGAGGTACCACTTTTTCTATTGTAAATTTGGTACCTCTTG[G/A]
TACCTAGGTACTATAAGGTATCATGAGGTACCAAATTTTATACTGAATTTTTGGTACCTCATAGTACCTCCTCAAGGACCGTAGATTTGCTCCTTCACGG

Reverse complement sequence

CCGTGAAGGAGCAAATCTACGGTCCTTGAGGAGGTACTATGAGGTACCAAAAATTCAGTATAAAATTTGGTACCTCATGATACCTTATAGTACCTAGGTA[C/T]
CAAGAGGTACCAAATTTACAATAGAAAAAGTGGTACCTCCTCAAGAGGTAGATGGATTGCACCGTAAGGACTAACTTGGTCAGGGTCGTTCTGCCTGCCG

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	38.50%	33.10%	0.93%	27.47%	NA
All Indica	2759	50.50%	23.20%	1.16%	25.19%	NA
All Japonica	1512	23.30%	42.50%	0.73%	33.47%	NA
Aus	269	10.80%	66.20%	0.37%	22.68%	NA
Indica I	595	27.40%	34.50%	2.52%	35.63%	NA
Indica II	465	83.00%	4.30%	1.29%	11.40%	NA
Indica III	913	51.20%	22.80%	0.33%	25.74%	NA
Indica Intermediate	786	47.80%	26.30%	1.02%	24.81%	NA
Temperate Japonica	767	32.10%	45.00%	0.26%	22.69%	NA
Tropical Japonica	504	8.70%	42.50%	0.79%	48.02%	NA
Japonica Intermediate	241	26.10%	34.40%	2.07%	37.34%	NA
VI/Aromatic	96	19.80%	68.80%	0.00%	11.46%	NA
Intermediate	90	30.00%	42.20%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127460166	G -> A	LOC_Os11g45380-LOC_Os11g45390	intergenic_region ; MODIFIER	silent_mutation	Average:25.302; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1127460166	G -> DEL	N	N	silent_mutation	Average:25.302; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127460166	NA	3.57E-07	mr1441	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
vg1127460166	2.46E-06	2.46E-06	mr1827	Ind_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
vg1127460166	NA	8.38E-07	mr1842	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
vg1127460166	NA	1.34E-07	mr1933_2	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