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Detailed information for vg1100087658:

Variant ID: vg1100087658 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 87658
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.21, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

AACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGGTAGGCTACTC[G/A]
TCACTTGTCTGCATGTTTTTGTTCTCAACTTATAAATATAATAGGTAGTTGATACCCCGCGCTTTGTTGCGGGATATGTATATGAATACATGCTATACAT

Reverse complement sequence

ATGTATAGCATGTATTCATATACATATCCCGCAACAAAGCGCGGGGTATCAACTACCTATTATATTTATAAGTTGAGAACAAAAACATGCAGACAAGTGA[C/T]
GAGTAGCCTACCACTTTTTGTATAATTTATGAGCTGAACTGTGACCTCTGCCTGGTTATCTATGGCATCTCTTATCTTCCTAACTGTTGCACGATCAGTT

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	56.90%	42.70%	0.08%	0.34%	NA
All Indica	2759	88.40%	11.50%	0.07%	0.00%	NA
All Japonica	1512	1.60%	97.40%	0.07%	0.99%	NA
Aus	269	68.80%	30.90%	0.37%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	55.70%	44.30%	0.00%	0.00%	NA
Indica III	913	96.40%	3.60%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.50%	0.25%	0.00%	NA
Temperate Japonica	767	1.30%	96.70%	0.00%	1.96%	NA
Tropical Japonica	504	1.80%	98.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	32.20%	66.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100087658	G -> A	LOC_Os11g01140.1	intron_variant ; MODIFIER	silent_mutation	Average:13.989; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg1100087658	G -> A	LOC_Os11g01140.2	intron_variant ; MODIFIER	silent_mutation	Average:13.989; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg1100087658	G -> A	LOC_Os11g01140.3	intron_variant ; MODIFIER	silent_mutation	Average:13.989; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg1100087658	G -> DEL	N	N	silent_mutation	Average:13.989; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100087658	NA	2.95E-06	mr1835	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
vg1100087658	NA	9.48E-10	mr1889	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
vg1100087658	NA	6.43E-09	mr1896	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
vg1100087658	NA	1.65E-08	mr1903	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
vg1100087658	NA	5.74E-11	mr1904	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
vg1100087658	NA	1.18E-13	mr1907	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
vg1100087658	NA	3.95E-10	mr1934	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
vg1100087658	NA	9.38E-09	mr1935	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
vg1100087658	NA	6.79E-11	mr1835_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
vg1100087658	2.56E-07	NA	mr1889_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
vg1100087658	1.55E-07	2.27E-16	mr1889_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
vg1100087658	NA	2.52E-09	mr1896_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
vg1100087658	NA	4.41E-15	mr1904_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
vg1100087658	3.50E-06	NA	mr1907_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
vg1100087658	NA	1.76E-14	mr1907_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
vg1100087658	NA	3.36E-11	mr1934_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