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Detailed information for vg0218470302:

Variant ID: vg0218470302 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18470302
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TTGACTCCCTCAACTGACCACCGAATCTAAATCGTATCCCTCAACTGCAATACCAGAAATCTCGACCCCCCGAACTTGCAAAACCGGTGCAATTTGACTC[C/T]
CTCAGCGGTTTTGGGGTGGTTTCGCTGATGTGGCGCCACGTGGCACCTATGTGGCGATATTGACCGAGTCTTCGGTCAACGTGGCGTTGGCGTGGCAGTA

Reverse complement sequence

TACTGCCACGCCAACGCCACGTTGACCGAAGACTCGGTCAATATCGCCACATAGGTGCCACGTGGCGCCACATCAGCGAAACCACCCCAAAACCGCTGAG[G/A]
GAGTCAAATTGCACCGGTTTTGCAAGTTCGGGGGGTCGAGATTTCTGGTATTGCAGTTGAGGGATACGATTTAGATTCGGTGGTCAGTTGAGGGAGTCAA

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 72.80% 26.10% 0.83% 0.28% NA
All Indica  2759 55.80% 43.10% 0.98% 0.14% NA
All Japonica  1512 97.60% 1.30% 0.53% 0.60% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 43.70% 55.10% 1.18% 0.00% NA
Indica II  465 46.90% 51.60% 1.08% 0.43% NA
Indica III  913 74.80% 24.30% 0.66% 0.22% NA
Indica Intermediate  786 48.10% 50.80% 1.15% 0.00% NA
Temperate Japonica  767 98.60% 1.30% 0.13% 0.00% NA
Tropical Japonica  504 96.80% 0.60% 1.39% 1.19% NA
Japonica Intermediate  241 95.90% 2.90% 0.00% 1.24% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 20.00% 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
vg0218470302 C -> T LOC_Os02g30930.1 upstream_gene_variant ; 4192.0bp to feature; MODIFIER silent_mutation Average:90.598; most accessible tissue: Zhenshan97 panicle, score: 95.438 N N N N
vg0218470302 C -> T LOC_Os02g30920.1 intron_variant ; MODIFIER silent_mutation Average:90.598; most accessible tissue: Zhenshan97 panicle, score: 95.438 N N N N
vg0218470302 C -> DEL N N silent_mutation Average:90.598; most accessible tissue: Zhenshan97 panicle, score: 95.438 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)
vg0218470302 C T 0.0 0.01 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218470302 NA 9.52E-08 mr1109 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
vg0218470302 NA 6.91E-06 mr1729 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
vg0218470302 NA 5.19E-06 mr1758 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
vg0218470302 NA 1.37E-19 mr1807 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
vg0218470302 NA 3.46E-09 mr1807 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
vg0218470302 NA 5.01E-09 mr1855 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
vg0218470302 NA 4.76E-06 mr1881 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
vg0218470302 NA 3.62E-06 mr1901 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
vg0218470302 NA 5.01E-07 mr1901 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
vg0218470302 NA 1.16E-06 mr1129_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
vg0218470302 NA 6.53E-07 mr1257_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
vg0218470302 NA 6.96E-08 mr1517_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
vg0218470302 NA 2.22E-07 mr1610_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
vg0218470302 NA 9.11E-13 mr1855_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
vg0218470302 NA 8.32E-15 mr1914_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
vg0218470302 NA 2.18E-09 mr1914_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
vg0218470302 NA 1.71E-09 mr1927_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