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Search for Variation information by Variation ID:

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

Detailed information for vg0620086973:

Variant ID: vg0620086973 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20086973
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCTATAGCTAAAAAAAACTAATTACAAGACTTCGTCAATCTCCAAGATAGATTTGTCGGCCCCTTCTTCGAAGATGTTTATAAGGGTGAGTGTGCGTG[T/C]
GTTGTGAGTATGTACGTTGTACTGTGTAATTTTTAAAAAAATTAGGTGAGAAAATTGAGGTAATAATCGAGGTGGATTGCCAGGCGAAAGCGACGATCAA

Reverse complement sequence

TTGATCGTCGCTTTCGCCTGGCAATCCACCTCGATTATTACCTCAATTTTCTCACCTAATTTTTTTAAAAATTACACAGTACAACGTACATACTCACAAC[A/G]
CACGCACACTCACCCTTATAAACATCTTCGAAGAAGGGGCCGACAAATCTATCTTGGAGATTGACGAAGTCTTGTAATTAGTTTTTTTTAGCTATAGGCC

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 65.60% 26.60% 0.06% 7.74% NA
All Indica  2759 95.00% 4.60% 0.04% 0.33% NA
All Japonica  1512 6.50% 72.50% 0.07% 20.97% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.60% 5.20% 0.17% 0.00% NA
Indica II  465 92.70% 6.00% 0.00% 1.29% NA
Indica III  913 99.30% 0.50% 0.00% 0.11% NA
Indica Intermediate  786 91.70% 8.00% 0.00% 0.25% NA
Temperate Japonica  767 6.00% 83.20% 0.13% 10.69% NA
Tropical Japonica  504 7.50% 69.80% 0.00% 22.62% NA
Japonica Intermediate  241 5.80% 44.00% 0.00% 50.21% NA
VI/Aromatic  96 66.70% 1.00% 1.04% 31.25% NA
Intermediate  90 54.40% 34.40% 0.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620086973 T -> C LOC_Os06g34510.1 upstream_gene_variant ; 2204.0bp to feature; MODIFIER silent_mutation Average:58.911; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg0620086973 T -> C LOC_Os06g34520.1 downstream_gene_variant ; 381.0bp to feature; MODIFIER silent_mutation Average:58.911; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg0620086973 T -> C LOC_Os06g34530.1 downstream_gene_variant ; 889.0bp to feature; MODIFIER silent_mutation Average:58.911; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg0620086973 T -> C LOC_Os06g34520-LOC_Os06g34530 intergenic_region ; MODIFIER silent_mutation Average:58.911; most accessible tissue: Zhenshan97 root, score: 87.373 N N N N
vg0620086973 T -> DEL N N silent_mutation Average:58.911; most accessible tissue: Zhenshan97 root, score: 87.373 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)
vg0620086973 T C -0.08 -0.1 -0.06 -0.02 -0.07 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620086973 NA 2.02E-15 mr1167 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
vg0620086973 NA 4.71E-07 mr1190 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
vg0620086973 NA 7.72E-06 mr1216 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
vg0620086973 NA 8.78E-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
vg0620086973 4.39E-06 4.39E-06 mr1267 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
vg0620086973 NA 2.68E-15 mr1324 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
vg0620086973 NA 3.37E-11 mr1325 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
vg0620086973 NA 8.18E-13 mr1326 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
vg0620086973 NA 4.36E-13 mr1335 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
vg0620086973 NA 8.72E-14 mr1478 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
vg0620086973 NA 9.36E-07 mr1527 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
vg0620086973 NA 2.13E-06 mr1532 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
vg0620086973 NA 3.33E-15 mr1675 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
vg0620086973 NA 5.54E-07 mr1677 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
vg0620086973 NA 3.64E-07 mr1690 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
vg0620086973 NA 9.65E-16 mr1726 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
vg0620086973 NA 3.83E-16 mr1950 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
vg0620086973 NA 1.46E-07 mr1979 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