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Detailed information for vg0414117579:

Variant ID: vg0414117579 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14117579
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GCCATCCCTCGAATCAAATCAGCGCATTCGGGTAGAATCAATGGCGGAAGAGAAAGAAAGCTTTGAAGGCCAATGGACGCCGTCCGACATAACAGAAGAG[C/A]
ACCTGAAGGAGATGGTGGCGCACGGCGTTCTCCCTGTCAAGGAGATCATCGGGTGGCGGCCAGCGTGCGGTGAGATTTTTCCGACCCCCGATACACACGA

Reverse complement sequence

TCGTGTGTATCGGGGGTCGGAAAAATCTCACCGCACGCTGGCCGCCACCCGATGATCTCCTTGACAGGGAGAACGCCGTGCGCCACCATCTCCTTCAGGT[G/T]
CTCTTCTGTTATGTCGGACGGCGTCCATTGGCCTTCAAAGCTTTCTTTCTCTTCCGCCATTGATTCTACCCGAATGCGCTGATTTGATTCGAGGGATGGC

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 46.20% 18.70% 29.05% 6.07% NA
All Indica  2759 33.50% 24.50% 32.62% 9.35% NA
All Japonica  1512 77.40% 9.10% 11.90% 1.59% NA
Aus  269 5.90% 5.20% 87.36% 1.49% NA
Indica I  595 56.10% 14.30% 22.35% 7.23% NA
Indica II  465 50.50% 13.10% 27.31% 9.03% NA
Indica III  913 12.40% 38.80% 38.88% 9.97% NA
Indica Intermediate  786 30.80% 22.50% 36.26% 10.43% NA
Temperate Japonica  767 95.80% 0.40% 2.87% 0.91% NA
Tropical Japonica  504 52.00% 24.20% 23.02% 0.79% NA
Japonica Intermediate  241 71.80% 5.40% 17.43% 5.39% NA
VI/Aromatic  96 25.00% 42.70% 32.29% 0.00% NA
Intermediate  90 54.40% 14.40% 30.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414117579 C -> DEL LOC_Os04g24580.1 N frameshift_variant Average:63.119; most accessible tissue: Minghui63 flag leaf, score: 89.812 N N N N
vg0414117579 C -> A LOC_Os04g24580.1 missense_variant ; p.His21Asn; MODERATE nonsynonymous_codon ; H21N Average:63.119; most accessible tissue: Minghui63 flag leaf, score: 89.812 probably damaging -2.616 TOLERATED 1.00

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)
vg0414117579 C A -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414117579 NA 6.23E-06 mr1045 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
vg0414117579 NA 7.00E-06 mr1170 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
vg0414117579 NA 7.69E-08 mr1729 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
vg0414117579 NA 5.84E-06 mr1793 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
vg0414117579 NA 2.32E-08 mr1173_2 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
vg0414117579 NA 1.65E-06 mr1358_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
vg0414117579 NA 1.13E-07 mr1749_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