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Detailed information for vg0223432768:

Variant ID: vg0223432768 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23432768
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGATGGTGCTTCGCCTTCCATGGTCGCCCTCCGCTCCGACGTCCTCCACGCCGTACGGCACCGCACCGCCGTCTCTCTCCCTCTCTCTCTCTCCATCCAT[C/T]
GGCCGGCTCCCCGCCTGCACGCCGGTAGCTGACGTGTTTTGGTTTTTCTTTTCTTTTCTTTTTTTATGCGGGGTTGGCTGCCGGACGACGCGCTGCTGGC

Reverse complement sequence

GCCAGCAGCGCGTCGTCCGGCAGCCAACCCCGCATAAAAAAAGAAAAGAAAAGAAAAACCAAAACACGTCAGCTACCGGCGTGCAGGCGGGGAGCCGGCC[G/A]
ATGGATGGAGAGAGAGAGAGGGAGAGAGACGGCGGTGCGGTGCCGTACGGCGTGGAGGACGTCGGAGCGGAGGGCGACCATGGAAGGCGAAGCACCATCA

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 83.80% 15.40% 0.19% 0.57% NA
All Indica  2759 87.40% 12.30% 0.25% 0.00% NA
All Japonica  1512 75.20% 24.60% 0.07% 0.13% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 72.30% 27.10% 0.66% 0.00% NA
Indica Intermediate  786 90.80% 9.00% 0.13% 0.00% NA
Temperate Japonica  767 81.40% 18.50% 0.13% 0.00% NA
Tropical Japonica  504 65.30% 34.70% 0.00% 0.00% NA
Japonica Intermediate  241 76.30% 22.80% 0.00% 0.83% NA
VI/Aromatic  96 75.00% 2.10% 0.00% 22.92% NA
Intermediate  90 80.00% 15.60% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0223432768 C -> T LOC_Os02g38780.1 intron_variant ; MODIFIER silent_mutation Average:87.304; most accessible tissue: Zhenshan97 flower, score: 93.532 N N N N
vg0223432768 C -> T LOC_Os02g38780.2 intron_variant ; MODIFIER silent_mutation Average:87.304; most accessible tissue: Zhenshan97 flower, score: 93.532 N N N N
vg0223432768 C -> T LOC_Os02g38780.3 intron_variant ; MODIFIER silent_mutation Average:87.304; most accessible tissue: Zhenshan97 flower, score: 93.532 N N N N
vg0223432768 C -> DEL N N silent_mutation Average:87.304; most accessible tissue: Zhenshan97 flower, score: 93.532 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)
vg0223432768 C T -0.02 -0.01 -0.05 0.01 -0.01 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223432768 NA 5.16E-06 mr1841 Jap_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