Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1105601806:

Variant ID: vg1105601806 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5601806
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTACGAAAGAATTATGGTCCAAGATAAGGTCTTCCAGCTGCCTACATTCTGAAAGAGATGACAAGAAGCCCATATTCCCCTCTAGGTTGTTGTGGGGT[A/G]
GAACGAGCTTCTGTAAAGCAGCAATGTTCCCCAGTGTCCGCGGTACCGAGCCAGACAACTGATTAGCTGAAAGAAGCAAGTACACAAGTTTCTGAAGTAA

Reverse complement sequence

TTACTTCAGAAACTTGTGTACTTGCTTCTTTCAGCTAATCAGTTGTCTGGCTCGGTACCGCGGACACTGGGGAACATTGCTGCTTTACAGAAGCTCGTTC[T/C]
ACCCCACAACAACCTAGAGGGGAATATGGGCTTCTTGTCATCTCTTTCAGAATGTAGGCAGCTGGAAGACCTTATCTTGGACCATAATTCTTTCGTAGGT

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 78.00% 12.30% 0.11% 9.61% NA
All Indica  2759 82.40% 11.80% 0.07% 5.73% NA
All Japonica  1512 86.40% 0.30% 0.07% 13.16% NA
Aus  269 7.40% 89.20% 0.37% 2.97% NA
Indica I  595 60.30% 26.60% 0.17% 12.94% NA
Indica II  465 96.30% 2.60% 0.00% 1.08% NA
Indica III  913 89.60% 5.40% 0.00% 5.04% NA
Indica Intermediate  786 82.40% 13.60% 0.13% 3.82% NA
Temperate Japonica  767 91.00% 0.00% 0.13% 8.87% NA
Tropical Japonica  504 88.30% 0.80% 0.00% 10.91% NA
Japonica Intermediate  241 68.00% 0.40% 0.00% 31.54% NA
VI/Aromatic  96 13.50% 2.10% 0.00% 84.38% NA
Intermediate  90 78.90% 11.10% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105601806 A -> DEL LOC_Os11g10310.1 N frameshift_variant Average:66.692; most accessible tissue: Minghui63 flag leaf, score: 81.052 N N N N
vg1105601806 A -> G LOC_Os11g10310.1 missense_variant ; p.Leu407Pro; MODERATE nonsynonymous_codon ; L407P Average:66.692; most accessible tissue: Minghui63 flag leaf, score: 81.052 benign 0.309 DELETERIOUS 0.00

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)
vg1105601806 A G 0.01 -0.01 0.0 0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105601806 NA 6.38E-07 mr1004 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
vg1105601806 NA 2.51E-07 mr1006 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
vg1105601806 NA 8.60E-06 mr1007 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
vg1105601806 NA 1.54E-07 mr1052 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
vg1105601806 NA 2.89E-07 mr1343 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
vg1105601806 NA 2.34E-08 mr1758 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
vg1105601806 NA 9.16E-14 mr1918 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
vg1105601806 NA 2.13E-08 mr1378_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
vg1105601806 NA 7.80E-08 mr1510_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
vg1105601806 NA 1.57E-08 mr1707_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
vg1105601806 NA 8.61E-09 mr1741_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
vg1105601806 NA 2.45E-11 mr1758_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
vg1105601806 NA 1.87E-08 mr1829_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