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Detailed information for vg0501832883:

Variant ID: vg0501832883 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1832883
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAAGCATCTTCCTTTTCGGGAGGATAATCCTATCGCAACTCCCTTGATATTTCTGCTAGTAATCACCCATGCTACTAAAAAGCAAGCACTAGGAAGGGG[C/T]
AACCATTGTTAAGCTCAAAAAGGGGAAGACGAAGAAGAACTGAAGAAGAGTTTGGGGTGATGGAGCTTGTCACCTCCACCATCTTGGCACGGAAGAAGGC

Reverse complement sequence

GCCTTCTTCCGTGCCAAGATGGTGGAGGTGACAAGCTCCATCACCCCAAACTCTTCTTCAGTTCTTCTTCGTCTTCCCCTTTTTGAGCTTAACAATGGTT[G/A]
CCCCTTCCTAGTGCTTGCTTTTTAGTAGCATGGGTGATTACTAGCAGAAATATCAAGGGAGTTGCGATAGGATTATCCTCCCGAAAAGGAAGATGCTTAC

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 94.20% 5.60% 0.17% 0.00% NA
All Indica  2759 90.40% 9.50% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 90.80% 9.00% 0.22% 0.00% NA
Indica III  913 84.60% 15.20% 0.22% 0.00% NA
Indica Intermediate  786 90.60% 9.20% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0501832883 C -> T LOC_Os05g04060.1 upstream_gene_variant ; 2832.0bp to feature; MODIFIER silent_mutation Average:63.73; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg0501832883 C -> T LOC_Os05g04070.1 intron_variant ; MODIFIER silent_mutation Average:63.73; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 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)
vg0501832883 C T 0.01 0.03 0.04 0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501832883 NA 5.77E-06 mr1122 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
vg0501832883 NA 1.59E-06 mr1671 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
vg0501832883 NA 1.09E-06 mr1713 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
vg0501832883 NA 7.98E-07 mr1720 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
vg0501832883 NA 9.65E-07 mr1321_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
vg0501832883 NA 1.95E-09 mr1322_2 Ind_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
vg0501832883 NA 1.66E-06 mr1325_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
vg0501832883 NA 4.80E-07 mr1326_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
vg0501832883 NA 7.65E-06 mr1623_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