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Detailed information for vg0219342960:

Variant ID: vg0219342960 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19342960
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, A: 0.32, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGGCCGCGATCGTGGACGGCGGCGGCCCGACGTACGCGCGCGTGGAGCCCGACGGCTACCTCGCCATGTACCAGAAGGAAGGGCCACCCGCCGAAGTC[C/A]
TCTCCTTCGACACCTTCAACCATGGCGTGCGGGCGCTCCGCCGCATGACGCTCGAGGCCGACGGCAACCTCCGCGCCTACTACTGGGACAGCACCGGCTC

Reverse complement sequence

GAGCCGGTGCTGTCCCAGTAGTAGGCGCGGAGGTTGCCGTCGGCCTCGAGCGTCATGCGGCGGAGCGCCCGCACGCCATGGTTGAAGGTGTCGAAGGAGA[G/T]
GACTTCGGCGGGTGGCCCTTCCTTCTGGTACATGGCGAGGTAGCCGTCGGGCTCCACGCGCGCGTACGTCGGGCCGCCGCCGTCCACGATCGCGGCCTTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 17.90% 0.02% 0.00% NA
All Indica  2759 78.30% 21.70% 0.04% 0.00% NA
All Japonica  1512 87.10% 12.90% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 92.40% 7.60% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 62.90% 37.00% 0.11% 0.00% NA
Indica Intermediate  786 77.70% 22.30% 0.00% 0.00% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 75.60% 24.40% 0.00% 0.00% NA
Japonica Intermediate  241 81.30% 18.70% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 0.00% 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
vg0219342960 C -> A LOC_Os02g32620.1 missense_variant ; p.Leu265Ile; MODERATE nonsynonymous_codon ; L265I Average:93.463; most accessible tissue: Zhenshan97 flag leaf, score: 96.129 benign 0.294 DELETERIOUS 0.04

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)
vg0219342960 C A 0.0 -0.01 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219342960 NA 9.13E-06 mr1063 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
vg0219342960 NA 8.02E-06 mr1213 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
vg0219342960 NA 6.78E-06 mr1215 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
vg0219342960 2.52E-06 2.52E-06 mr1460 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
vg0219342960 NA 7.46E-06 mr1215_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
vg0219342960 NA 6.05E-06 mr1220_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
vg0219342960 NA 8.64E-06 mr1381_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
vg0219342960 NA 5.10E-07 mr1661_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
vg0219342960 NA 3.65E-06 mr1696_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