Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1103105609:

Variant ID: vg1103105609 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 3105609
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGCCCGGCCACCGCTATCTTCGACGCCCGCCGCACGGCCACCGCCGTCTTCCACCTCCACTGCCATCTCCTGCGTCTGCCACTGCCGTCTTCCGTTGT[C/T]
GGTGACAGCGAATCGAAGCTAGCTCAAGAAAGAAGAAGACATGAAGACATGAACTAAGGGGATAGGAGGGAGAAAGAGAATGTGAGGTAGGAGAAGATGG

Reverse complement sequence

CCATCTTCTCCTACCTCACATTCTCTTTCTCCCTCCTATCCCCTTAGTTCATGTCTTCATGTCTTCTTCTTTCTTGAGCTAGCTTCGATTCGCTGTCACC[G/A]
ACAACGGAAGACGGCAGTGGCAGACGCAGGAGATGGCAGTGGAGGTGGAAGACGGCGGTGGCCGTGCGGCGGGCGTCGAAGATAGCGGTGGCCGGGCCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 5.50% 1.50% 0.00% NA
All Indica  2759 93.10% 5.40% 1.41% 0.00% NA
All Japonica  1512 96.10% 2.20% 1.72% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 87.20% 8.40% 4.37% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 93.50% 6.20% 0.22% 0.00% NA
Indica Intermediate  786 93.60% 5.10% 1.27% 0.00% NA
Temperate Japonica  767 97.30% 0.40% 2.35% 0.00% NA
Tropical Japonica  504 95.20% 4.40% 0.40% 0.00% NA
Japonica Intermediate  241 94.20% 3.30% 2.49% 0.00% NA
VI/Aromatic  96 26.00% 71.90% 2.08% 0.00% NA
Intermediate  90 88.90% 6.70% 4.44% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1103105609 C -> T LOC_Os11g06430.1 missense_variant ; p.Asp67Asn; MODERATE nonsynonymous_codon ; D67N Average:75.961; most accessible tissue: Zhenshan97 panicle, score: 92.533 unknown unknown 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)
vg1103105609 C T 0.01 0.01 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1103105609 1.14E-06 NA mr1409 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
vg1103105609 NA 1.51E-07 mr1585_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