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Detailed information for vg0504458914:

Variant ID: vg0504458914 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4458914
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCATCTTGGACATCGGATTCCTATTGACAAACCCATTAACGTATAATGGCTTAAGGTGCCGATTTTCTGTCCCCTCTGGCTTCTCAAAGATTGCTTG[C/T]
TCTAGTGACAAAATCAACATAGCAGAGGCCTCCTCTACATCATCAACATCGGCTTCTTTAGCTTCAAATTCTACAGGAAGCATGGAGACCATGTTCACCG

Reverse complement sequence

CGGTGAACATGGTCTCCATGCTTCCTGTAGAATTTGAAGCTAAAGAAGCCGATGTTGATGATGTAGAGGAGGCCTCTGCTATGTTGATTTTGTCACTAGA[G/A]
CAAGCAATCTTTGAGAAGCCAGAGGGGACAGAAAATCGGCACCTTAAGCCATTATACGTTAATGGGTTTGTCAATAGGAATCCGATGTCCAAGATGATGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.10%	41.70%	8.17%	1.99%	NA
All Indica	2759	18.90%	69.00%	11.63%	0.43%	NA
All Japonica	1512	93.70%	0.80%	1.39%	4.17%	NA
Aus	269	78.40%	8.20%	8.18%	5.20%	NA
Indica I	595	20.70%	67.10%	11.93%	0.34%	NA
Indica II	465	25.80%	61.70%	11.83%	0.65%	NA
Indica III	913	11.70%	77.10%	11.06%	0.11%	NA
Indica Intermediate	786	21.90%	65.40%	11.96%	0.76%	NA
Temperate Japonica	767	98.80%	0.90%	0.13%	0.13%	NA
Tropical Japonica	504	86.50%	0.80%	3.17%	9.52%	NA
Japonica Intermediate	241	92.10%	0.40%	1.66%	5.81%	NA
VI/Aromatic	96	66.70%	14.60%	16.67%	2.08%	NA
Intermediate	90	68.90%	21.10%	6.67%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504458914	C -> T	LOC_Os05g08170.1	synonymous_variant ; p.Glu493Glu; LOW	synonymous_codon	Average:12.73; most accessible tissue: Callus, score: 35.786	N	N	N	N
vg0504458914	C -> DEL	LOC_Os05g08170.1	N	frameshift_variant	Average:12.73; most accessible tissue: Callus, score: 35.786	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504458914	NA	2.00E-44	mr1721	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
vg0504458914	NA	9.19E-06	mr1053_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
vg0504458914	NA	3.15E-55	mr1109_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
vg0504458914	NA	7.17E-36	mr1129_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
vg0504458914	NA	1.28E-14	mr1147_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
vg0504458914	NA	3.18E-17	mr1199_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
vg0504458914	NA	7.48E-22	mr1253_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
vg0504458914	NA	1.40E-20	mr1255_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
vg0504458914	NA	5.34E-29	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
vg0504458914	NA	4.52E-22	mr1316_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
vg0504458914	1.62E-06	1.62E-06	mr1367_2	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
vg0504458914	NA	4.69E-06	mr1825_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
vg0504458914	NA	2.92E-06	mr1925_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
vg0504458914	NA	6.39E-61	mr1970_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