Search for Variation information by Variation ID:

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

Detailed information for vg0725235447:

Variant ID: vg0725235447 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25235447
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAACTTCTAATTTTTCCATCACATTAAAACTTTCCTATACACACAAACTTCCAACTTTTCCATCATATCATTCCAATTTCAATCAAACTTCCAATTTT[G/A]
GCGTGAACTAAACACACCCCAAGTTTGTTTGAAGTTAGGCACGCTAAGTTTGAAAGCTTAGATTGAAACATTGTCCACTAGGACACATGTCATTACGTCA

Reverse complement sequence

TGACGTAATGACATGTGTCCTAGTGGACAATGTTTCAATCTAAGCTTTCAAACTTAGCGTGCCTAACTTCAAACAAACTTGGGGTGTGTTTAGTTCACGC[C/T]
AAAATTGGAAGTTTGATTGAAATTGGAATGATATGATGGAAAAGTTGGAAGTTTGTGTGTATAGGAAAGTTTTAATGTGATGGAAAAATTAGAAGTTTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.80% 42.70% 0.19% 0.30% NA
All Indica  2759 77.10% 22.30% 0.18% 0.47% NA
All Japonica  1512 33.80% 66.10% 0.13% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 81.00% 18.70% 0.34% 0.00% NA
Indica II  465 77.20% 21.90% 0.22% 0.65% NA
Indica III  913 77.40% 21.70% 0.00% 0.88% NA
Indica Intermediate  786 73.70% 25.80% 0.25% 0.25% NA
Temperate Japonica  767 61.50% 38.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.80% 0.20% 0.00% NA
Japonica Intermediate  241 14.10% 85.50% 0.41% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 37.80% 58.90% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0725235447 G -> DEL N N silent_mutation Average:71.867; most accessible tissue: Zhenshan97 flower, score: 91.792 N N N N
vg0725235447 G -> A LOC_Os07g42180.1 upstream_gene_variant ; 4318.0bp to feature; MODIFIER silent_mutation Average:71.867; most accessible tissue: Zhenshan97 flower, score: 91.792 N N N N
vg0725235447 G -> A LOC_Os07g42170.1 downstream_gene_variant ; 1214.0bp to feature; MODIFIER silent_mutation Average:71.867; most accessible tissue: Zhenshan97 flower, score: 91.792 N N N N
vg0725235447 G -> A LOC_Os07g42160-LOC_Os07g42170 intergenic_region ; MODIFIER silent_mutation Average:71.867; most accessible tissue: Zhenshan97 flower, score: 91.792 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)
vg0725235447 G A 0.01 0.01 0.01 0.02 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725235447 3.07E-06 NA mr1933 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
vg0725235447 NA 1.61E-12 mr1189_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
vg0725235447 NA 1.51E-09 mr1338_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
vg0725235447 NA 3.63E-07 mr1346_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
vg0725235447 NA 7.91E-06 mr1428_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
vg0725235447 NA 1.01E-08 mr1642_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
vg0725235447 NA 1.60E-10 mr1734_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
vg0725235447 NA 1.44E-07 mr1815_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
vg0725235447 NA 1.55E-06 mr1966_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
vg0725235447 NA 3.82E-06 mr1992_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