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Detailed information for vg0428450154:

Variant ID: vg0428450154 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28450154
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCTATTGTGGTACAGAGTACTCCCTCCGTCCAAAAAAAACTCAACTTCTAGAGTTTGAATTTTGTCATACAAAAAACCAACTTCTACCATCCTACCTAT[C/A]
CTCAGCACGTAAAATGAGAAGTTTTGTCCCTTCAATACCCTTTACTTAGCTATCACTCTTATTACTTTTTTTAATGATTAAGAATATTTTAGTCATTTTT

Reverse complement sequence

AAAAATGACTAAAATATTCTTAATCATTAAAAAAAGTAATAAGAGTGATAGCTAAGTAAAGGGTATTGAAGGGACAAAACTTCTCATTTTACGTGCTGAG[G/T]
ATAGGTAGGATGGTAGAAGTTGGTTTTTTGTATGACAAAATTCAAACTCTAGAAGTTGAGTTTTTTTTGGACGGAGGGAGTACTCTGTACCACAATAGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.00% 7.30% 0.66% 0.00% NA
All Indica  2759 99.40% 0.60% 0.04% 0.00% NA
All Japonica  1512 76.90% 21.20% 1.92% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 70.50% 26.20% 3.26% 0.00% NA
Tropical Japonica  504 90.50% 8.90% 0.60% 0.00% NA
Japonica Intermediate  241 68.90% 30.70% 0.41% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 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
vg0428450154 C -> A LOC_Os04g47870-LOC_Os04g47890 intergenic_region ; MODIFIER silent_mutation Average:54.207; most accessible tissue: Zhenshan97 panicle, score: 90.467 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)
vg0428450154 C A -0.01 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428450154 8.16E-12 6.03E-28 Awn_length All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0428450154 NA 1.63E-08 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0428450154 NA 4.52E-11 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0428450154 NA 1.69E-12 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652