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Detailed information for vg0601214662:

Variant ID: vg0601214662 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1214662
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.16, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ACACAGGCTCACATAAATCAGGGTTGCGTTTTAGGGAAGAGGTCGTTCAATAATTTGTAAGAGCAAGTTTAATAGTACAGTCCAACTACTGACTCCAATT[T/C]
ATCTATATATAATCTAATAGCTCATTTATACAATAGTTACATACTACACTATTAATATCTGGTCCCACCTGTCATACACACACTGCGTCTTGGAGTCCGT

Reverse complement sequence

ACGGACTCCAAGACGCAGTGTGTGTATGACAGGTGGGACCAGATATTAATAGTGTAGTATGTAACTATTGTATAAATGAGCTATTAGATTATATATAGAT[A/G]
AATTGGAGTCAGTAGTTGGACTGTACTATTAAACTTGCTCTTACAAATTATTGAACGACCTCTTCCCTAAAACGCAACCCTGATTTATGTGAGCCTGTGT

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 50.80% 45.00% 0.23% 3.94% NA
All Indica  2759 62.70% 30.40% 0.36% 6.60% NA
All Japonica  1512 20.60% 79.20% 0.00% 0.13% NA
Aus  269 94.80% 4.80% 0.37% 0.00% NA
Indica I  595 92.40% 7.20% 0.34% 0.00% NA
Indica II  465 46.90% 44.30% 0.43% 8.39% NA
Indica III  913 51.60% 37.90% 0.44% 10.08% NA
Indica Intermediate  786 62.30% 30.90% 0.25% 6.49% NA
Temperate Japonica  767 11.30% 88.70% 0.00% 0.00% NA
Tropical Japonica  504 40.90% 58.70% 0.00% 0.40% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 64.60% 35.40% 0.00% 0.00% NA
Intermediate  90 48.90% 48.90% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0601214662 T -> C LOC_Os06g03210.1 downstream_gene_variant ; 4211.0bp to feature; MODIFIER silent_mutation Average:66.344; most accessible tissue: Minghui63 panicle, score: 93.176 N N N N
vg0601214662 T -> C LOC_Os06g03220.1 downstream_gene_variant ; 3802.0bp to feature; MODIFIER silent_mutation Average:66.344; most accessible tissue: Minghui63 panicle, score: 93.176 N N N N
vg0601214662 T -> C LOC_Os06g03210-LOC_Os06g03220 intergenic_region ; MODIFIER silent_mutation Average:66.344; most accessible tissue: Minghui63 panicle, score: 93.176 N N N N
vg0601214662 T -> DEL N N silent_mutation Average:66.344; most accessible tissue: Minghui63 panicle, score: 93.176 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)
vg0601214662 T C 0.03 -0.01 -0.01 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601214662 NA 1.30E-10 Grain_weight 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
vg0601214662 5.66E-07 2.77E-09 mr1141_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
vg0601214662 NA 1.95E-09 mr1399_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