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Detailed information for vg1214657491:

Variant ID: vg1214657491 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14657491
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGAACCGTTTGGCCCATTTCGCCGCAAACCTCTAGCATGCCCCAAACCGTCTGGCGTGAGGGGAGGCAACGGGCTCCCGAGGTCAGGGGCAAGTTTTA[T/C]
AGTGGAGGTGAGTGCCACATCTAATTTATACCATATCATCTTCTCATTAATTAAGAGGTAACAAGTACAACATATTACCTCTAGTACACAAACCCCAATA

Reverse complement sequence

TATTGGGGTTTGTGTACTAGAGGTAATATGTTGTACTTGTTACCTCTTAATTAATGAGAAGATGATATGGTATAAATTAGATGTGGCACTCACCTCCACT[A/G]
TAAAACTTGCCCCTGACCTCGGGAGCCCGTTGCCTCCCCTCACGCCAGACGGTTTGGGGCATGCTAGAGGTTTGCGGCGAAATGGGCCAAACGGTTCGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.80% 10.80% 1.33% 17.03% NA
All Indica  2759 54.70% 15.30% 1.41% 28.56% NA
All Japonica  1512 93.30% 5.20% 1.32% 0.26% NA
Aus  269 98.90% 0.70% 0.00% 0.37% NA
Indica I  595 31.60% 46.70% 2.02% 19.66% NA
Indica II  465 63.90% 4.50% 1.51% 30.11% NA
Indica III  913 59.10% 2.70% 0.66% 37.46% NA
Indica Intermediate  786 61.60% 12.60% 1.78% 24.05% NA
Temperate Japonica  767 96.20% 2.20% 1.17% 0.39% NA
Tropical Japonica  504 89.50% 9.10% 1.39% 0.00% NA
Japonica Intermediate  241 91.70% 6.20% 1.66% 0.41% NA
VI/Aromatic  96 89.60% 1.00% 0.00% 9.38% NA
Intermediate  90 85.60% 6.70% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214657491 T -> C LOC_Os12g25409.1 upstream_gene_variant ; 2670.0bp to feature; MODIFIER silent_mutation Average:92.625; most accessible tissue: Callus, score: 97.742 N N N N
vg1214657491 T -> C LOC_Os12g25400.1 downstream_gene_variant ; 4522.0bp to feature; MODIFIER silent_mutation Average:92.625; most accessible tissue: Callus, score: 97.742 N N N N
vg1214657491 T -> C LOC_Os12g25400-LOC_Os12g25409 intergenic_region ; MODIFIER silent_mutation Average:92.625; most accessible tissue: Callus, score: 97.742 N N N N
vg1214657491 T -> DEL N N silent_mutation Average:92.625; most accessible tissue: Callus, score: 97.742 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)
vg1214657491 T C 0.17 0.12 0.12 0.13 0.14 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214657491 NA 1.35E-10 mr1018 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
vg1214657491 NA 2.12E-11 mr1055 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
vg1214657491 NA 7.92E-11 mr1132 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
vg1214657491 NA 9.01E-09 mr1156 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
vg1214657491 NA 6.02E-06 mr1164 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
vg1214657491 NA 4.93E-06 mr1179 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
vg1214657491 1.62E-07 1.62E-07 mr1184 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
vg1214657491 NA 2.30E-07 mr1236 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
vg1214657491 NA 1.91E-11 mr1390 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
vg1214657491 NA 1.02E-11 mr1490 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
vg1214657491 NA 4.28E-12 mr1055_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
vg1214657491 NA 3.10E-14 mr1132_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
vg1214657491 NA 2.26E-06 mr1164_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
vg1214657491 NA 2.47E-07 mr1170_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
vg1214657491 NA 7.05E-14 mr1178_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
vg1214657491 NA 4.41E-08 mr1261_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
vg1214657491 1.11E-06 NA mr1291_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
vg1214657491 NA 1.69E-07 mr1308_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
vg1214657491 5.72E-06 4.79E-09 mr1361_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
vg1214657491 NA 2.04E-16 mr1390_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
vg1214657491 NA 1.75E-14 mr1490_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
vg1214657491 NA 6.12E-06 mr1511_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
vg1214657491 NA 6.45E-08 mr1676_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
vg1214657491 NA 2.56E-06 mr1745_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