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Detailed information for vg1002316286:

Variant ID: vg1002316286 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2316286
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.19, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGAGCACCGGTGTTGGTGCCCGCGTCTGTGGTGGGTGCAGTGGCGGTGTTGCGGGGAGATATGGAGGTGCGCCAGAGGCGGACGATGGTGAGGAAGGC[C/T]
GCCACCGTTGTTCCCCCATTCCCCTATCCGTCTCTTATGACTCCCTCCCCTTTCTTGCAGTGCGGCGGTGGCGGTGGTTTGGGCGGAGAAGGCCACGGCA

Reverse complement sequence

TGCCGTGGCCTTCTCCGCCCAAACCACCGCCACCGCCGCACTGCAAGAAAGGGGAGGGAGTCATAAGAGACGGATAGGGGAATGGGGGAACAACGGTGGC[G/A]
GCCTTCCTCACCATCGTCCGCCTCTGGCGCACCTCCATATCTCCCCGCAACACCGCCACTGCACCCACCACAGACGCGGGCACCAACACCGGTGCTCCAC

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 63.10% 36.60% 0.34% 0.00% NA
All Indica  2759 56.00% 43.60% 0.47% 0.00% NA
All Japonica  1512 68.70% 31.20% 0.13% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 62.40% 37.50% 0.17% 0.00% NA
Indica II  465 35.30% 64.10% 0.65% 0.00% NA
Indica III  913 66.50% 33.20% 0.33% 0.00% NA
Indica Intermediate  786 51.10% 48.10% 0.76% 0.00% NA
Temperate Japonica  767 58.00% 41.90% 0.13% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 49.00% 50.60% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 1.11% 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
vg1002316286 C -> T LOC_Os10g04800.1 upstream_gene_variant ; 1007.0bp to feature; MODIFIER silent_mutation Average:79.207; most accessible tissue: Minghui63 young leaf, score: 89.557 N N N N
vg1002316286 C -> T LOC_Os10g04810.1 downstream_gene_variant ; 3178.0bp to feature; MODIFIER silent_mutation Average:79.207; most accessible tissue: Minghui63 young leaf, score: 89.557 N N N N
vg1002316286 C -> T LOC_Os10g04780-LOC_Os10g04800 intergenic_region ; MODIFIER silent_mutation Average:79.207; most accessible tissue: Minghui63 young leaf, score: 89.557 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)
vg1002316286 C T -0.01 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002316286 NA 2.79E-06 mr1547 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
vg1002316286 NA 5.61E-07 mr1547 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
vg1002316286 NA 8.80E-07 mr1709 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
vg1002316286 9.59E-07 NA mr1713 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
vg1002316286 NA 4.22E-06 mr1713 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
vg1002316286 NA 1.33E-10 mr1709_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
vg1002316286 NA 4.99E-08 mr1709_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
vg1002316286 NA 7.69E-06 mr1768_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