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Detailed information for vg0408211190:

Variant ID: vg0408211190 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8211190
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCCGCGTTCGCCGGTGGCTCCGGCCCATGTTCTTTTTTTTTTTTTTAGAATTACACAGTACAACGCAGACACTCACAACGCACGCGCACTCACCCCTA[C/T]
AAACACACGCACGCAAACCCTACCCCTATGAGCATCTTCGAAGACTGTGCCGGCAAATCCTGTAGAGATTGACGAAGTCACCACAGGCGACTCGCTGTCG

Reverse complement sequence

CGACAGCGAGTCGCCTGTGGTGACTTCGTCAATCTCTACAGGATTTGCCGGCACAGTCTTCGAAGATGCTCATAGGGGTAGGGTTTGCGTGCGTGTGTTT[G/A]
TAGGGGTGAGTGCGCGTGCGTTGTGAGTGTCTGCGTTGTACTGTGTAATTCTAAAAAAAAAAAAAAGAACATGGGCCGGAGCCACCGGCGAACGCGGGAG

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 20.70% 3.70% 0.44% 75.14% NA
All Indica  2759 1.30% 5.60% 0.65% 92.42% NA
All Japonica  1512 61.00% 1.00% 0.00% 38.03% NA
Aus  269 0.40% 0.00% 0.37% 99.26% NA
Indica I  595 0.50% 0.00% 0.67% 98.82% NA
Indica II  465 2.40% 21.70% 0.86% 75.05% NA
Indica III  913 0.70% 3.00% 0.55% 95.84% NA
Indica Intermediate  786 2.20% 3.30% 0.64% 93.89% NA
Temperate Japonica  767 96.00% 0.00% 0.00% 4.04% NA
Tropical Japonica  504 6.50% 0.40% 0.00% 93.06% NA
Japonica Intermediate  241 63.50% 5.40% 0.00% 31.12% NA
VI/Aromatic  96 0.00% 0.00% 0.00% 100.00% NA
Intermediate  90 21.10% 6.70% 2.22% 70.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408211190 C -> DEL N N silent_mutation Average:80.278; most accessible tissue: Zhenshan97 young leaf, score: 94.586 N N N N
vg0408211190 C -> T LOC_Os04g14640.1 downstream_gene_variant ; 3465.0bp to feature; MODIFIER silent_mutation Average:80.278; most accessible tissue: Zhenshan97 young leaf, score: 94.586 N N N N
vg0408211190 C -> T LOC_Os04g14640-LOC_Os04g14654 intergenic_region ; MODIFIER silent_mutation Average:80.278; most accessible tissue: Zhenshan97 young leaf, score: 94.586 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)
vg0408211190 C T 0.01 0.03 0.02 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408211190 NA 2.07E-18 mr1077 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
vg0408211190 NA 1.02E-06 mr1077 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
vg0408211190 NA 2.76E-06 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
vg0408211190 NA 3.72E-22 mr1300 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
vg0408211190 NA 2.05E-34 mr1310 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
vg0408211190 NA 2.38E-85 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
vg0408211190 NA 4.99E-15 mr1401 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
vg0408211190 NA 2.29E-10 mr1471 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
vg0408211190 NA 1.42E-24 mr1679 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
vg0408211190 NA 5.56E-09 mr1691 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
vg0408211190 NA 3.53E-10 mr1693 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
vg0408211190 NA 3.21E-07 mr1715 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
vg0408211190 NA 8.75E-14 mr1740 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
vg0408211190 NA 3.64E-32 mr1789 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
vg0408211190 NA 7.58E-13 mr1844 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
vg0408211190 NA 2.23E-42 mr1926 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
vg0408211190 NA 2.95E-12 mr1520_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
vg0408211190 NA 9.52E-08 mr1526_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
vg0408211190 NA 2.05E-22 mr1679_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