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Detailed information for vg0600689387:

Variant ID: vg0600689387 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 689387
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAGAGCTAGCAGGGTGAAGAAGAAATACTATACTCCATTAGTTCATTTTTATAGTGTTTGTTTATTTTAAAATCTATTTTCAAAACAATACCGCGCT[T/C]
ATATTCACGTTCGTACACTCACTTCTAAACTCATACACATACACTTTATCTCTATGAGTATGCACTTTTAAAGACTGGATCAACGTATCTTAAAATTGAA

Reverse complement sequence

TTCAATTTTAAGATACGTTGATCCAGTCTTTAAAAGTGCATACTCATAGAGATAAAGTGTATGTGTATGAGTTTAGAAGTGAGTGTACGAACGTGAATAT[A/G]
AGCGCGGTATTGTTTTGAAAATAGATTTTAAAATAAACAAACACTATAAAAATGAACTAATGGAGTATAGTATTTCTTCTTCACCCTGCTAGCTCTTCTT

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 62.60% 37.40% 0.00% 0.00% NA
All Indica  2759 92.60% 7.40% 0.00% 0.00% NA
All Japonica  1512 7.90% 92.10% 0.00% 0.00% NA
Aus  269 84.80% 15.20% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 81.30% 18.70% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 7.90% 0.00% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 21.60% 78.40% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0600689387 T -> C LOC_Os06g02220.1 upstream_gene_variant ; 3367.0bp to feature; MODIFIER silent_mutation Average:85.678; most accessible tissue: Minghui63 flower, score: 92.413 N N N N
vg0600689387 T -> C LOC_Os06g02210-LOC_Os06g02220 intergenic_region ; MODIFIER silent_mutation Average:85.678; most accessible tissue: Minghui63 flower, score: 92.413 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)
vg0600689387 T C -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600689387 NA 2.29E-07 mr1425 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
vg0600689387 5.88E-07 1.24E-10 mr1518 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
vg0600689387 NA 7.56E-06 mr1600 Jap_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
vg0600689387 NA 7.79E-08 mr1676 Jap_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
vg0600689387 NA 5.14E-10 mr1141_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
vg0600689387 NA 4.23E-09 mr1676_2 Jap_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