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Detailed information for vg1221083115:

Variant ID: vg1221083115 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21083115
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TCAACTAGCGGGAGGCGGGGCTGGGATACCCAGGGTGTTCGAGCCCAAGGTAAGCCCAACACTGCTCATGCGGTTTGGCGGGTTCATGGTGGAGGGATCC[G/A]
ACATGGGTGGTCCATGCGGGATTTGCTTCTGAATCCGATTGAGGAGGTTGCTATCCCCGCAAGGTGGGTCTGGGTCCCGAAGGGGAGGTCTCTAAGTCCG

Reverse complement sequence

CGGACTTAGAGACCTCCCCTTCGGGACCCAGACCCACCTTGCGGGGATAGCAACCTCCTCAATCGGATTCAGAAGCAAATCCCGCATGGACCACCCATGT[C/T]
GGATCCCTCCACCATGAACCCGCCAAACCGCATGAGCAGTGTTGGGCTTACCTTGGGCTCGAACACCCTGGGTATCCCAGCCCCGCCTCCCGCTAGTTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.90% 30.50% 0.13% 28.52% NA
All Indica  2759 48.40% 11.20% 0.14% 40.27% NA
All Japonica  1512 31.90% 66.50% 0.00% 1.65% NA
Aus  269 3.00% 27.10% 0.74% 69.14% NA
Indica I  595 79.50% 12.40% 0.17% 7.90% NA
Indica II  465 37.80% 21.70% 0.00% 40.43% NA
Indica III  913 36.00% 2.00% 0.11% 61.88% NA
Indica Intermediate  786 45.50% 14.60% 0.25% 39.57% NA
Temperate Japonica  767 6.00% 93.40% 0.00% 0.65% NA
Tropical Japonica  504 74.60% 22.20% 0.00% 3.17% NA
Japonica Intermediate  241 24.90% 73.40% 0.00% 1.66% NA
VI/Aromatic  96 70.80% 16.70% 0.00% 12.50% NA
Intermediate  90 42.20% 42.20% 0.00% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1221083115 G -> DEL LOC_Os12g34720.1 N frameshift_variant Average:67.853; most accessible tissue: Zhenshan97 young leaf, score: 87.299 N N N N
vg1221083115 G -> A LOC_Os12g34720.1 missense_variant ; p.Arg76Gln; MODERATE nonsynonymous_codon ; R76Q Average:67.853; most accessible tissue: Zhenshan97 young leaf, score: 87.299 unknown unknown TOLERATED 0.08

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1221083115 G A -0.01 -0.02 -0.01 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221083115 NA 5.83E-07 mr1013 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
vg1221083115 NA 2.55E-06 mr1034 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
vg1221083115 NA 5.14E-11 mr1093 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
vg1221083115 NA 3.62E-07 mr1121 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
vg1221083115 NA 5.62E-11 mr1235 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
vg1221083115 NA 1.81E-09 mr1251 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
vg1221083115 NA 4.38E-06 mr1257 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
vg1221083115 6.15E-26 3.72E-117 mr1334 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
vg1221083115 2.99E-08 6.22E-10 mr1334 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
vg1221083115 1.52E-12 3.73E-28 mr1334 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
vg1221083115 NA 3.49E-08 mr1423 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
vg1221083115 NA 3.73E-11 mr1435 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
vg1221083115 NA 4.41E-07 mr1471 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
vg1221083115 NA 2.09E-10 mr1539 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
vg1221083115 NA 3.24E-08 mr1599 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
vg1221083115 NA 2.93E-07 mr1642 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
vg1221083115 NA 9.91E-06 mr1686 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
vg1221083115 NA 8.45E-06 mr1817 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
vg1221083115 NA 9.64E-08 mr1864 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
vg1221083115 NA 4.17E-09 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
vg1221083115 NA 1.67E-12 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
vg1221083115 1.41E-30 5.54E-128 mr1334_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
vg1221083115 4.89E-10 1.58E-08 mr1334_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
vg1221083115 9.04E-13 8.08E-34 mr1334_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
vg1221083115 NA 1.24E-07 mr1607_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
vg1221083115 NA 3.25E-08 mr1817_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
vg1221083115 NA 3.46E-11 mr1830_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
vg1221083115 NA 4.48E-06 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
vg1221083115 3.97E-09 2.11E-53 mr1991_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
vg1221083115 1.03E-07 2.61E-14 mr1991_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