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Detailed information for vg0418090060:

Variant ID: vg0418090060 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18090060
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGGAATTGATTATTTCAGAGGTTTTCCTGACTTCCTCTTGTTGGGCCTGCCCCACAATGATTAGATCATCTGCAAACATCAGAGAATGAATGGAAGGA[T/C]
CATTTTGTCCTAACTTTATTCCTGAAATGTGGTTCCTTTGAATTGCATCTGCAAGCTGGTCAGAAAGTTCATTAATCGCAAGGACAAAAAGATAAGGCGA

Reverse complement sequence

TCGCCTTATCTTTTTGTCCTTGCGATTAATGAACTTTCTGACCAGCTTGCAGATGCAATTCAAAGGAACCACATTTCAGGAATAAAGTTAGGACAAAATG[A/G]
TCCTTCCATTCATTCTCTGATGTTTGCAGATGATCTAATCATTGTGGGGCAGGCCCAACAAGAGGAAGTCAGGAAAACCTCTGAAATAATCAATTCCTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.50% 0.30% 26.53% 18.71% NA
All Indica  2759 31.00% 0.30% 42.08% 26.60% NA
All Japonica  1512 93.30% 0.10% 3.84% 2.78% NA
Aus  269 56.10% 0.70% 6.69% 36.43% NA
Indica I  595 45.40% 0.30% 17.82% 36.47% NA
Indica II  465 51.60% 0.40% 37.85% 10.11% NA
Indica III  913 10.70% 0.40% 54.98% 33.84% NA
Indica Intermediate  786 31.40% 0.10% 47.96% 20.48% NA
Temperate Japonica  767 99.20% 0.00% 0.00% 0.78% NA
Tropical Japonica  504 90.50% 0.20% 2.98% 6.35% NA
Japonica Intermediate  241 80.50% 0.00% 17.84% 1.66% NA
VI/Aromatic  96 89.60% 0.00% 4.17% 6.25% NA
Intermediate  90 81.10% 0.00% 14.44% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0418090060 T -> C LOC_Os04g30300.1 missense_variant ; p.Asp342Gly; MODERATE nonsynonymous_codon ; D342G Average:21.413; most accessible tissue: Zhenshan97 flower, score: 88.727 unknown unknown TOLERATED 1.00
vg0418090060 T -> DEL LOC_Os04g30300.1 N frameshift_variant Average:21.413; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N

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)
vg0418090060 T C 0.03 0.03 0.0 0.03 0.13 0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418090060 NA 3.17E-06 mr1066 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
vg0418090060 NA 1.53E-07 mr1242 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
vg0418090060 3.59E-06 3.59E-06 mr1571 Jap_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
vg0418090060 NA 8.93E-08 mr1851 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
vg0418090060 8.44E-06 2.98E-08 mr1851 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
vg0418090060 NA 4.13E-06 mr1864 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
vg0418090060 NA 5.40E-06 mr1496_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