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Detailed information for vg0613451204:

Variant ID: vg0613451204 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13451204
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.56, A: 0.44, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GAGACAGCGTATCATGCCATACTCGGGCGCCCGGCGTTAGCCAAATTTATGGCTGTCTTGCACTATACCTACATGATGATGAAGATGCCTGGTCCTCGAG[A/G]
AGTCATATCCCTGCGGAGTGACATCAAACAAGCCGTCACATGCGATAAGGAAAGCTGCGAGATGGCCCAAACTCGCGAGATCACGATCGCCCGAGAAGAC

Reverse complement sequence

GTCTTCTCGGGCGATCGTGATCTCGCGAGTTTGGGCCATCTCGCAGCTTTCCTTATCGCATGTGACGGCTTGTTTGATGTCACTCCGCAGGGATATGACT[T/C]
CTCGAGGACCAGGCATCTTCATCATCATGTAGGTATAGTGCAAGACAGCCATAAATTTGGCTAACGCCGGGCGCCCGAGTATGGCATGATACGCTGTCTC

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	59.10%	31.00%	2.16%	7.68%	NA
All Indica	2759	82.00%	2.70%	3.23%	12.07%	NA
All Japonica	1512	10.00%	89.70%	0.07%	0.26%	NA
Aus	269	87.40%	1.50%	2.97%	8.18%	NA
Indica I	595	87.90%	2.90%	2.02%	7.23%	NA
Indica II	465	86.50%	3.90%	1.29%	8.39%	NA
Indica III	913	74.70%	0.70%	4.60%	20.04%	NA
Indica Intermediate	786	83.50%	4.20%	3.69%	8.65%	NA
Temperate Japonica	767	3.10%	96.20%	0.13%	0.52%	NA
Tropical Japonica	504	21.20%	78.80%	0.00%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	56.70%	34.40%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613451204	A -> G	LOC_Os06g23070.1	missense_variant ; p.Glu591Gly; MODERATE	nonsynonymous_codon ; E591G	Average:46.864; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	benign	-0.901	TOLERATED	1.00
vg0613451204	A -> DEL	LOC_Os06g23070.1	N	frameshift_variant	Average:46.864; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613451204	2.89E-21	4.62E-90	mr1033	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
vg0613451204	4.56E-14	3.39E-20	mr1033	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
vg0613451204	3.61E-15	1.22E-49	mr1176	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
vg0613451204	2.93E-11	1.36E-14	mr1176	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
vg0613451204	NA	6.37E-15	mr1276	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
vg0613451204	NA	2.84E-20	mr1477	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
vg0613451204	1.33E-07	5.82E-72	mr1536	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
vg0613451204	1.60E-07	1.60E-07	mr1536	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
vg0613451204	NA	6.25E-21	mr1971	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
vg0613451204	1.04E-29	1.15E-124	mr1033_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
vg0613451204	9.83E-17	5.64E-26	mr1033_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
vg0613451204	NA	9.07E-20	mr1276_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
vg0613451204	7.10E-08	NA	mr1536_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
vg0613451204	NA	2.69E-09	mr1536_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
vg0613451204	NA	1.18E-08	mr1660_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