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Detailed information for vg1215343863:

Variant ID: vg1215343863 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15343863
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCGTTAGTCTCGTCTAGTCAGCAAGTCGAAGGTGGAGTCTAACCGTGAATCGTCAATGGATTAATTAGGCTTAATAAATTCATCTCGCGATTTATAGA[T/C]
GCAATCTGCAATTAGTTTTTTTATTAGTATCCGAAATCTCTATGAAACATCCGATTTGACACCCTAAAATTTTATACACCTAACACTAATTAAACATCCC

Reverse complement sequence

GGGATGTTTAATTAGTGTTAGGTGTATAAAATTTTAGGGTGTCAAATCGGATGTTTCATAGAGATTTCGGATACTAATAAAAAAACTAATTGCAGATTGC[A/G]
TCTATAAATCGCGAGATGAATTTATTAAGCCTAATTAATCCATTGACGATTCACGGTTAGACTCCACCTTCGACTTGCTGACTAGACGAGACTAACGACG

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 25.10% 9.50% 6.03% 59.46% NA
All Indica  2759 3.60% 12.40% 8.92% 75.17% NA
All Japonica  1512 67.50% 2.60% 1.98% 27.84% NA
Aus  269 6.70% 19.70% 1.49% 72.12% NA
Indica I  595 2.00% 17.50% 18.82% 61.68% NA
Indica II  465 4.30% 3.40% 6.24% 86.02% NA
Indica III  913 1.90% 13.00% 5.04% 80.07% NA
Indica Intermediate  786 6.20% 13.00% 7.51% 73.28% NA
Temperate Japonica  767 91.10% 0.70% 0.26% 7.95% NA
Tropical Japonica  504 34.30% 5.60% 4.96% 55.16% NA
Japonica Intermediate  241 61.80% 2.90% 1.24% 34.02% NA
VI/Aromatic  96 10.40% 6.20% 2.08% 81.25% NA
Intermediate  90 41.10% 7.80% 3.33% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215343863 T -> C LOC_Os12g26290.1 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26300.1 upstream_gene_variant ; 4253.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290.2 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290.3 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290.4 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290.5 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290.6 upstream_gene_variant ; 3358.0bp to feature; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> C LOC_Os12g26290-LOC_Os12g26300 intergenic_region ; MODIFIER silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg1215343863 T -> DEL N N silent_mutation Average:93.528; most accessible tissue: Minghui63 young leaf, score: 99.097 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)
vg1215343863 T C 0.07 0.03 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215343863 8.36E-06 NA mr1016 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
vg1215343863 9.74E-07 2.02E-17 mr1016 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
vg1215343863 1.13E-06 NA mr1017 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
vg1215343863 4.61E-06 8.03E-17 mr1017 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
vg1215343863 8.97E-06 NA mr1018 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
vg1215343863 1.87E-06 1.34E-16 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
vg1215343863 3.22E-06 2.62E-14 mr1019 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
vg1215343863 NA 9.27E-13 mr1022 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
vg1215343863 NA 2.90E-18 mr1023 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
vg1215343863 4.31E-08 NA mr1055 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
vg1215343863 3.16E-08 5.04E-20 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
vg1215343863 4.31E-06 NA mr1079 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
vg1215343863 1.41E-07 7.80E-23 mr1079 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
vg1215343863 4.30E-06 NA mr1132 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
vg1215343863 3.29E-07 5.09E-20 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
vg1215343863 9.74E-07 NA mr1142 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
vg1215343863 1.45E-06 2.75E-21 mr1142 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
vg1215343863 7.28E-06 3.82E-17 mr1178 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
vg1215343863 NA 2.42E-10 mr1282 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
vg1215343863 1.93E-06 NA mr1390 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
vg1215343863 5.86E-10 1.86E-23 mr1390 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
vg1215343863 1.78E-07 NA mr1489 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
vg1215343863 2.45E-06 4.06E-20 mr1489 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
vg1215343863 1.89E-07 NA mr1490 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
vg1215343863 1.76E-10 1.31E-23 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
vg1215343863 4.72E-06 5.67E-20 mr1491 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
vg1215343863 NA 7.79E-06 mr1531 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
vg1215343863 NA 7.48E-10 mr1658 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
vg1215343863 2.87E-06 NA mr1778 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
vg1215343863 NA 9.92E-18 mr1778 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
vg1215343863 NA 1.79E-09 mr1942 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
vg1215343863 NA 6.68E-12 mr1019_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
vg1215343863 4.27E-06 1.20E-16 mr1022_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
vg1215343863 4.15E-07 NA mr1023_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
vg1215343863 3.78E-07 1.99E-28 mr1023_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
vg1215343863 NA 6.87E-15 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
vg1215343863 1.23E-07 NA mr1079_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
vg1215343863 2.33E-07 2.64E-25 mr1079_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
vg1215343863 NA 1.56E-20 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
vg1215343863 NA 9.94E-21 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
vg1215343863 NA 6.29E-11 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
vg1215343863 NA 6.45E-06 mr1265_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
vg1215343863 1.97E-06 1.71E-21 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
vg1215343863 1.99E-06 NA mr1489_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
vg1215343863 NA 2.60E-23 mr1489_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
vg1215343863 9.85E-06 NA mr1490_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
vg1215343863 1.12E-06 9.35E-22 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
vg1215343863 NA 4.10E-09 mr1607_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
vg1215343863 NA 2.23E-18 mr1778_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
vg1215343863 NA 2.76E-15 mr1942_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