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Detailed information for vg1000283563:

Variant ID: vg1000283563 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 283563
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTTAAATATTTAGGGACGGAGGGAGTATATGGTAGTTGGTATTCCATCCGTTCAAAGATATTTTCGCTACATATATAGGAACCTTTTGAAAAGATTAA[T/G]
GATTATGATGCAAAGTCAAAAATATTCTCATTATAGAGGTAGGTTGGTAGTGTGATATATAGTAGATCGTTAGGGGTGGAAAGAGAAAATAATTGATAAA

Reverse complement sequence

TTTATCAATTATTTTCTCTTTCCACCCCTAACGATCTACTATATATCACACTACCAACCTACCTCTATAATGAGAATATTTTTGACTTTGCATCATAATC[A/C]
TTAATCTTTTCAAAAGGTTCCTATATATGTAGCGAAAATATCTTTGAACGGATGGAATACCAACTACCATATACTCCCTCCGTCCCTAAATATTTAACGC

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 88.80% 11.10% 0.11% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 66.20% 33.50% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 37.40% 61.90% 0.65% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1000283563 T -> G LOC_Os10g01460.1 upstream_gene_variant ; 1023.0bp to feature; MODIFIER silent_mutation Average:84.913; most accessible tissue: Zhenshan97 flower, score: 92.936 N N N N
vg1000283563 T -> G LOC_Os10g01470.1 downstream_gene_variant ; 1138.0bp to feature; MODIFIER silent_mutation Average:84.913; most accessible tissue: Zhenshan97 flower, score: 92.936 N N N N
vg1000283563 T -> G LOC_Os10g01460-LOC_Os10g01470 intergenic_region ; MODIFIER silent_mutation Average:84.913; most accessible tissue: Zhenshan97 flower, score: 92.936 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)
vg1000283563 T G -0.04 -0.02 -0.02 0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000283563 1.01E-07 2.76E-23 mr1300 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
vg1000283563 7.69E-07 NA mr1310 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
vg1000283563 NA 4.86E-07 mr1310 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
vg1000283563 8.35E-11 5.82E-42 mr1926 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
vg1000283563 NA 1.13E-08 mr1926 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
vg1000283563 NA 8.30E-12 mr1959 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
vg1000283563 3.76E-07 NA mr1168_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
vg1000283563 3.34E-06 3.34E-06 mr1168_2 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
vg1000283563 1.98E-11 8.26E-40 mr1310_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
vg1000283563 NA 2.95E-10 mr1310_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
vg1000283563 5.50E-10 2.78E-23 mr1959_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
vg1000283563 NA 4.32E-09 mr1959_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