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Detailed information for vg0612563052:

Variant ID: vg0612563052 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12563052
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


AGAATCCCCCATGATTTCGATAGCACCGGCTTCAACTTCCTTTAGTAACTGCAACCCCTTGAGGACCGCCTCATACTCAGCTTGATTATTAGTCGCATAA[A/G]
GTTTAATAGTATAAGCAAACTCAAAACATGCCCCCCGAGGGGAAATTATAACTAAGCCGATACCACAACCATGAGTACAAACTGACCCATCAAAGAATAA

Reverse complement sequence

TTATTCTTTGATGGGTCAGTTTGTACTCATGGTTGTGGTATCGGCTTAGTTATAATTTCCCCTCGGGGGGCATGTTTTGAGTTTGCTTATACTATTAAAC[T/C]
TTATGCGACTAATAATCAAGCTGAGTATGAGGCGGTCCTCAAGGGGTTGCAGTTACTAAAGGAAGTTGAAGCCGGTGCTATCGAAATCATGGGGGATTCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.00% 34.50% 16.46% 9.99% NA
All Indica  2759 57.60% 5.50% 25.37% 11.56% NA
All Japonica  1512 0.90% 88.70% 1.52% 8.86% NA
Aus  269 70.60% 16.00% 9.67% 3.72% NA
Indica I  595 47.20% 8.90% 32.94% 10.92% NA
Indica II  465 62.60% 4.50% 26.67% 6.24% NA
Indica III  913 64.40% 1.50% 19.50% 14.57% NA
Indica Intermediate  786 54.60% 8.00% 25.70% 11.70% NA
Temperate Japonica  767 0.30% 96.30% 1.43% 1.96% NA
Tropical Japonica  504 1.60% 76.60% 1.59% 20.24% NA
Japonica Intermediate  241 1.70% 89.60% 1.66% 7.05% NA
VI/Aromatic  96 27.10% 58.30% 10.42% 4.17% NA
Intermediate  90 28.90% 44.40% 21.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0612563052 A -> G LOC_Os06g21740.1 missense_variant ; p.Leu1012Pro; MODERATE nonsynonymous_codon ; L1012P Average:11.111; most accessible tissue: Callus, score: 44.196 possibly damaging -1.818 TOLERATED 1.00
vg0612563052 A -> DEL LOC_Os06g21740.1 N frameshift_variant Average:11.111; most accessible tissue: Callus, score: 44.196 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612563052 NA 6.42E-30 mr1072 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
vg0612563052 NA 2.08E-06 mr1072 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
vg0612563052 NA 5.75E-29 mr1075 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
vg0612563052 2.75E-07 NA mr1100 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
vg0612563052 4.78E-08 1.63E-08 mr1100 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
vg0612563052 NA 3.05E-31 mr1202 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
vg0612563052 NA 4.58E-07 mr1202 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
vg0612563052 NA 1.11E-06 mr1395 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
vg0612563052 NA 5.07E-06 mr1426 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
vg0612563052 NA 1.96E-51 mr1795 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
vg0612563052 NA 4.27E-54 mr1861 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
vg0612563052 5.54E-06 7.52E-07 mr1861 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
vg0612563052 NA 2.40E-23 mr1888 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
vg0612563052 NA 6.32E-15 mr1933 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
vg0612563052 NA 1.58E-09 mr1222_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