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Detailed information for vg0514203146:

Variant ID: vg0514203146 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14203146
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.23, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCTCTGCTGGGAAAATGGATATGGAATTTGGAAAACAAAGAAGTTTGGTGGCAAGATATACTTAGGGATAAGTATCTGAGAAAAAAACCCCTCTCTGA[G/A]
GTTAAGAATAAAATGGGGGACTCTCACTTTTGGCAAGGTTTATTGGAGATTAAAAACACCTTTTACAAATTCTGTACTAAGAAACTGGGAGATGGCAAAC

Reverse complement sequence

GTTTGCCATCTCCCAGTTTCTTAGTACAGAATTTGTAAAAGGTGTTTTTAATCTCCAATAAACCTTGCCAAAAGTGAGAGTCCCCCATTTTATTCTTAAC[C/T]
TCAGAGAGGGGTTTTTTTCTCAGATACTTATCCCTAAGTATATCTTGCCACCAAACTTCTTTGTTTTCCAAATTCCATATCCATTTTCCCAGCAGAGCAG

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	55.50%	44.20%	0.21%	0.02%	NA
All Indica	2759	92.00%	7.90%	0.11%	0.04%	NA
All Japonica	1512	2.50%	97.40%	0.13%	0.00%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	96.10%	3.90%	0.00%	0.00%	NA
Indica II	465	95.70%	4.10%	0.00%	0.22%	NA
Indica III	913	88.60%	11.20%	0.22%	0.00%	NA
Indica Intermediate	786	90.60%	9.30%	0.13%	0.00%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.20%	0.20%	0.00%	NA
Japonica Intermediate	241	1.20%	98.30%	0.41%	0.00%	NA
VI/Aromatic	96	0.00%	99.00%	1.04%	0.00%	NA
Intermediate	90	47.80%	47.80%	4.44%	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
vg0514203146	G -> DEL	LOC_Os05g24610.1	N	frameshift_variant	Average:38.096; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0514203146	G -> A	LOC_Os05g24610.1	synonymous_variant ; p.Glu1502Glu; LOW	synonymous_codon	Average:38.096; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514203146	NA	1.95E-06	mr1071	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
vg0514203146	NA	3.58E-13	mr1329	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
vg0514203146	NA	5.34E-11	mr1524	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
vg0514203146	NA	3.69E-25	mr1537	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
vg0514203146	NA	8.94E-13	mr1657	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
vg0514203146	NA	7.69E-16	mr1700	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
vg0514203146	NA	6.65E-11	mr1720	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
vg0514203146	NA	1.87E-31	mr1745	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
vg0514203146	NA	6.54E-12	mr1914	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
vg0514203146	NA	1.55E-28	mr1039_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
vg0514203146	NA	1.08E-26	mr1270_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
vg0514203146	NA	8.71E-14	mr1514_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
vg0514203146	NA	1.96E-39	mr1745_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
vg0514203146	NA	4.57E-30	mr1932_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