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Detailed information for vg0810585964:

Variant ID: vg0810585964 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10585964
Reference Allele: TAlternative Allele: G,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGAAGCCTGAGGAGGCCGTCGCCGCTCCACGTCGCGACGACCCCGCCGATGCTCCATCGGGGGAGCTCCTTGACGCCGGCAGAGCTCGTCGTCGTCTTC[T/G,A]
TCCTCTACGCGCCGGTCGTGAGTGGGAGAGCCAGCACCGGTGGAGGGAGAAGGGGGACGCCGGCCAATCTCGCGATGGATTTGGGGGAGAAACCGCGCAC

Reverse complement sequence

GTGCGCGGTTTCTCCCCCAAATCCATCGCGAGATTGGCCGGCGTCCCCCTTCTCCCTCCACCGGTGCTGGCTCTCCCACTCACGACCGGCGCGTAGAGGA[A/C,T]
GAAGACGACGACGAGCTCTGCCGGCGTCAAGGAGCTCCCCCGATGGAGCATCGGCGGGGTCGTCGCGACGTGGAGCGGCGACGGCCTCCTCAGGCTTCCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 8.80% 1.63% 0.00% A: 0.06%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 67.90% 27.00% 5.09% 0.00% NA
Aus  269 98.90% 0.00% 0.00% 0.00% A: 1.12%
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 43.20% 48.10% 8.74% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 81.70% 14.50% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0810585964 T -> G LOC_Os08g17294-LOC_Os08g17320 intergenic_region ; MODIFIER silent_mutation Average:83.455; most accessible tissue: Zhenshan97 young leaf, score: 91.689 N N N N
vg0810585964 T -> A LOC_Os08g17294-LOC_Os08g17320 intergenic_region ; MODIFIER silent_mutation Average:83.455; most accessible tissue: Zhenshan97 young leaf, score: 91.689 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)
vg0810585964 T A -0.2 -0.13 -0.12 -0.11 -0.15 -0.17
vg0810585964 T G -0.14 -0.09 -0.07 -0.09 -0.11 -0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810585964 NA 6.41E-10 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
vg0810585964 NA 1.22E-15 Spikelet_length 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
vg0810585964 4.32E-07 NA mr1525 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
vg0810585964 NA 4.41E-06 mr1942 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
vg0810585964 NA 1.22E-09 mr1002_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
vg0810585964 NA 6.91E-10 mr1011_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
vg0810585964 NA 1.15E-06 mr1011_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
vg0810585964 NA 9.14E-06 mr1206_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
vg0810585964 NA 1.37E-07 mr1229_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
vg0810585964 NA 6.54E-07 mr1229_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
vg0810585964 NA 8.79E-07 mr1252_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
vg0810585964 NA 1.10E-06 mr1263_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
vg0810585964 NA 4.15E-07 mr1263_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
vg0810585964 NA 8.75E-07 mr1555_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
vg0810585964 NA 1.98E-06 mr1588_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
vg0810585964 NA 3.17E-06 mr1763_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
vg0810585964 NA 1.51E-09 mr1880_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
vg0810585964 NA 1.23E-08 mr1880_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