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Detailed information for vg0722874861:

Variant ID: vg0722874861 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22874861
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTGTAGCTGAGGTCCAGCGTCTGCAGCGTGGAGAGCGCGGCGAGGGAGCGTGGCACGGTGCCCCTGATGCGGTTGTGGCTGAGGTCCAGGTAGGTGAG[C/T]
TCCGGCGGGAAGACGAGCTTGCTGAGGTCGAAGTCGAGGTCGTTCCACGAGAGGTCCACCTTGCCGATGGGCCGGCCGGCGGCGAAGAGGAAGGAGGCGT

Reverse complement sequence

ACGCCTCCTTCCTCTTCGCCGCCGGCCGGCCCATCGGCAAGGTGGACCTCTCGTGGAACGACCTCGACTTCGACCTCAGCAAGCTCGTCTTCCCGCCGGA[G/A]
CTCACCTACCTGGACCTCAGCCACAACCGCATCAGGGGCACCGTGCCACGCTCCCTCGCCGCGCTCTCCACGCTGCAGACGCTGGACCTCAGCTACAACC

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 58.80% 40.80% 0.06% 0.32% NA
All Indica  2759 32.10% 67.30% 0.11% 0.47% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.07% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 4.50% 95.00% 0.17% 0.34% NA
Indica II  465 48.20% 51.00% 0.00% 0.86% NA
Indica III  913 40.20% 59.60% 0.00% 0.22% NA
Indica Intermediate  786 34.00% 65.10% 0.25% 0.64% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 0.00% 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
vg0722874861 C -> DEL LOC_Os07g38130.1 N frameshift_variant Average:88.861; most accessible tissue: Minghui63 panicle, score: 99.482 N N N N
vg0722874861 C -> T LOC_Os07g38130.1 synonymous_variant ; p.Glu262Glu; LOW synonymous_codon Average:88.861; most accessible tissue: Minghui63 panicle, score: 99.482 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)
vg0722874861 C T 0.0 -0.02 -0.02 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722874861 NA 9.33E-06 mr1189 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
vg0722874861 NA 9.36E-14 mr1531 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
vg0722874861 NA 5.60E-06 mr1679 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
vg0722874861 NA 7.13E-07 mr1796 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
vg0722874861 NA 4.36E-07 mr1990 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
vg0722874861 NA 5.46E-06 mr1679_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
vg0722874861 NA 1.25E-08 mr1962_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