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Detailed information for vg0728374173:

Variant ID: vg0728374173 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28374173
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAATTCCCACCCCTCGAACTTGCATATCTGTCACCAACATCTCTGCAGCCTCCATCTGCCCAATCTTGCAGAACCCATTGATCAATGCTCCATACGTA[T/C]
GCTCGTTTGGCTCAATGCCATTCCCAACACATTCATCAAACACCTCCGATGCCCTCCGCACATTCCCTGCACGGCAGTATGCGTTGATGACTGAAGAATA

Reverse complement sequence

TATTCTTCAGTCATCAACGCATACTGCCGTGCAGGGAATGTGCGGAGGGCATCGGAGGTGTTTGATGAATGTGTTGGGAATGGCATTGAGCCAAACGAGC[A/G]
TACGTATGGAGCATTGATCAATGGGTTCTGCAAGATTGGGCAGATGGAGGCTGCAGAGATGTTGGTGACAGATATGCAAGTTCGAGGGGTGGGAATTAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.00% 6.00% 0.00% 0.00% NA
All Indica  2759 90.90% 9.10% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 91.00% 9.00% 0.00% 0.00% NA
Indica III  913 86.00% 14.00% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0728374173 T -> C LOC_Os07g47470.1 missense_variant ; p.His284Arg; MODERATE nonsynonymous_codon ; H284R Average:80.974; most accessible tissue: Zhenshan97 young leaf, score: 89.226 benign -0.433 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)
vg0728374173 T C -0.02 -0.02 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728374173 NA 9.72E-07 mr1411 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
vg0728374173 NA 1.06E-06 mr1518 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
vg0728374173 NA 1.60E-09 mr1546 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
vg0728374173 NA 1.50E-06 mr1970_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