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Detailed information for vg0919877661:

Variant ID: vg0919877661 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19877661
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGGAGGCCTGAACTATAGATCAAATTTCATTCACATTCCTCAAGCTTAATTTTTTTTTATAGAATTACACCGTACAATATAGATACTCACAACGCACG[C/T]
GCACTTATCCTTATGAACACACGCACGCAAACCCTACCTCCATGAGTATCTTCGAAGATTAGGCCAGCAAATCCTGAAAAAAATGACAATGTAAATCGAG

Reverse complement sequence

CTCGATTTACATTGTCATTTTTTTCAGGATTTGCTGGCCTAATCTTCGAAGATACTCATGGAGGTAGGGTTTGCGTGCGTGTGTTCATAAGGATAAGTGC[G/A]
CGTGCGTTGTGAGTATCTATATTGTACGGTGTAATTCTATAAAAAAAAATTAAGCTTGAGGAATGTGAATGAAATTTGATCTATAGTTCAGGCCTCCAAG

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 92.00% 7.80% 0.19% 0.00% NA
All Indica  2759 98.70% 1.20% 0.11% 0.00% NA
All Japonica  1512 79.40% 20.20% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.40% 0.38% 0.00% NA
Temperate Japonica  767 99.10% 0.70% 0.26% 0.00% NA
Tropical Japonica  504 41.10% 58.10% 0.79% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0919877661 C -> T LOC_Os09g33660.1 missense_variant ; p.Arg37Cys; MODERATE nonsynonymous_codon ; R37C Average:94.895; most accessible tissue: Minghui63 root, score: 96.882 unknown unknown DELETERIOUS 0.01

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)
vg0919877661 C T 0.02 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919877661 NA 5.49E-07 mr1642 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
vg0919877661 NA 2.53E-08 mr1742 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
vg0919877661 5.07E-09 NA mr1745 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
vg0919877661 NA 4.19E-07 mr1696_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
vg0919877661 4.86E-10 NA mr1745_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
vg0919877661 NA 9.92E-06 mr1786_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