Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0623460564:

Variant ID: vg0623460564 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23460564
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGCGACACAGTCTTTAAAATACAACTTTAATTTCTTGTTTCTATAAAAATATTTATTGAAAAGTGATATATGTATACTTTTATGAAAGTATTTTTAAGA[T/C]
AAATCTATTCATATAATTTTTACATTTGCAAACTCAACAACTTGAGAGTTATTCATAATTTATATTCCTAAGATTTGACTTAAACATTGTTCTAAACAAT

Reverse complement sequence

ATTGTTTAGAACAATGTTTAAGTCAAATCTTAGGAATATAAATTATGAATAACTCTCAAGTTGTTGAGTTTGCAAATGTAAAAATTATATGAATAGATTT[A/G]
TCTTAAAAATACTTTCATAAAAGTATACATATATCACTTTTCAATAAATATTTTTATAGAAACAAGAAATTAAAGTTGTATTTTAAAGACTGTGTCGCTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.60% 0.30% 1.50% 26.66% NA
All Indica  2759 97.20% 0.00% 0.11% 2.72% NA
All Japonica  1512 22.80% 0.90% 1.46% 74.93% NA
Aus  269 98.90% 0.00% 0.00% 1.12% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 94.40% 0.00% 0.00% 5.59% NA
Indica III  913 97.80% 0.00% 0.22% 1.97% NA
Indica Intermediate  786 96.10% 0.00% 0.13% 3.82% NA
Temperate Japonica  767 36.10% 0.90% 0.65% 62.32% NA
Tropical Japonica  504 7.50% 0.60% 3.17% 88.69% NA
Japonica Intermediate  241 12.00% 1.20% 0.41% 86.31% NA
VI/Aromatic  96 28.10% 0.00% 44.79% 27.08% NA
Intermediate  90 71.10% 0.00% 3.33% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0623460564 T -> C LOC_Os06g39510.1 downstream_gene_variant ; 3661.0bp to feature; MODIFIER silent_mutation Average:76.101; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0623460564 T -> C LOC_Os06g39515.1 intron_variant ; MODIFIER silent_mutation Average:76.101; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0623460564 T -> DEL N N silent_mutation Average:76.101; most accessible tissue: Minghui63 young leaf, score: 93.766 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)
vg0623460564 T C 0.01 0.0 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623460564 NA 1.52E-11 mr1070 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
vg0623460564 NA 5.37E-11 mr1097 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
vg0623460564 NA 1.07E-09 mr1198 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
vg0623460564 NA 7.71E-07 mr1245 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
vg0623460564 NA 1.62E-06 mr1278 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
vg0623460564 NA 1.41E-08 mr1302 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
vg0623460564 NA 5.21E-07 mr1315 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
vg0623460564 NA 8.15E-06 mr1373 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
vg0623460564 NA 5.60E-07 mr1392 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
vg0623460564 NA 1.67E-06 mr1418 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
vg0623460564 NA 5.76E-08 mr1420 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
vg0623460564 NA 2.09E-08 mr1442 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
vg0623460564 NA 1.37E-08 mr1488 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
vg0623460564 NA 4.06E-08 mr1506 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
vg0623460564 NA 2.95E-06 mr1508 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
vg0623460564 NA 3.25E-13 mr1521 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
vg0623460564 NA 2.45E-07 mr1604 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
vg0623460564 NA 1.28E-12 mr1641 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
vg0623460564 NA 4.40E-07 mr1680 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
vg0623460564 NA 1.16E-13 mr1751 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
vg0623460564 NA 1.60E-07 mr1764 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
vg0623460564 NA 4.29E-07 mr1797 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
vg0623460564 NA 4.29E-07 mr1801 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
vg0623460564 NA 4.74E-07 mr1810 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
vg0623460564 NA 5.76E-07 mr1824 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
vg0623460564 NA 4.02E-06 mr1832 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