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Detailed information for vg0419252093:

Variant ID: vg0419252093 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19252093
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAAACATACATGAAAATAATAATATAATGAATAATCTAATTCAAATGCGCAAGTGTTGCTATCAGGGCAATCCCAACCCTCCACCTAGGAGTCTATGG[T/C]
ATTAACTACATTGCCATGTAAGATTTTTAGCTTATGTGGCACTATATTAATTAAGAGAGAGAGTGAAGAGAGGAAGAAACTGGGTCTCATACAAGACACA

Reverse complement sequence

TGTGTCTTGTATGAGACCCAGTTTCTTCCTCTCTTCACTCTCTCTCTTAATTAATATAGTGCCACATAAGCTAAAAATCTTACATGGCAATGTAGTTAAT[A/G]
CCATAGACTCCTAGGTGGAGGGTTGGGATTGCCCTGATAGCAACACTTGCGCATTTGAATTAGATTATTCATTATATTATTATTTTCATGTATGTTTGAT

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 53.90% 44.20% 1.65% 0.30% NA
All Indica  2759 83.10% 14.10% 2.39% 0.47% NA
All Japonica  1512 2.20% 97.40% 0.40% 0.00% NA
Aus  269 71.00% 27.50% 1.12% 0.37% NA
Indica I  595 81.30% 13.10% 5.38% 0.17% NA
Indica II  465 60.60% 38.50% 0.86% 0.00% NA
Indica III  913 96.40% 1.30% 1.31% 0.99% NA
Indica Intermediate  786 82.20% 15.10% 2.29% 0.38% NA
Temperate Japonica  767 1.30% 98.00% 0.65% 0.00% NA
Tropical Japonica  504 2.60% 97.20% 0.20% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 16.70% 80.00% 3.33% 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
vg0419252093 T -> C LOC_Os04g32090-LOC_Os04g32100 intergenic_region ; MODIFIER silent_mutation Average:80.139; most accessible tissue: Zhenshan97 young leaf, score: 97.112 N N N N
vg0419252093 T -> DEL N N silent_mutation Average:80.139; most accessible tissue: Zhenshan97 young leaf, score: 97.112 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)
vg0419252093 T C -0.06 -0.04 -0.03 0.0 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419252093 NA 7.30E-06 mr1189 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
vg0419252093 NA 7.24E-16 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
vg0419252093 NA 5.30E-12 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
vg0419252093 NA 3.41E-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
vg0419252093 NA 1.42E-13 mr1521 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
vg0419252093 1.52E-12 1.93E-13 mr1851 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
vg0419252093 1.17E-08 7.64E-11 mr1851 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
vg0419252093 1.98E-07 6.53E-14 mr1864 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
vg0419252093 3.10E-06 4.48E-09 mr1864 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
vg0419252093 NA 1.40E-06 mr1062_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
vg0419252093 NA 3.48E-24 mr1195_2 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
vg0419252093 NA 1.87E-09 mr1195_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
vg0419252093 NA 4.00E-13 mr1521_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
vg0419252093 NA 6.98E-08 mr1576_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
vg0419252093 NA 1.55E-09 mr1851_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