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Detailed information for vg0104343872:

Variant ID: vg0104343872 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4343872
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TCAACATCAAGGAGGAGTTCAAATGGTTTTTGAGAAATTCAAATCTGAAATAGTAGATTTGATTGAATTCAATCAAAATTTGGTTCGACATCTGGCTGGC[A/G]
GCAGCAGCAGCAGCAGAAGAACTATTACCTCCAAAATATACTCCTTGAAGTGAACTGTCCACTGTCGATGGAACAAAAAATGTTTGTCTCCAACGAGGTC

Reverse complement sequence

GACCTCGTTGGAGACAAACATTTTTTGTTCCATCGACAGTGGACAGTTCACTTCAAGGAGTATATTTTGGAGGTAATAGTTCTTCTGCTGCTGCTGCTGC[T/C]
GCCAGCCAGATGTCGAACCAAATTTTGATTGAATTCAATCAAATCTACTATTTCAGATTTGAATTTCTCAAAAACCATTTGAACTCCTCCTTGATGTTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.40% 17.40% 1.12% 50.13% NA
All Indica  2759 14.80% 1.60% 1.63% 81.99% NA
All Japonica  1512 47.90% 48.60% 0.26% 3.17% NA
Aus  269 92.60% 0.00% 0.00% 7.43% NA
Indica I  595 4.00% 0.00% 2.18% 93.78% NA
Indica II  465 6.50% 1.30% 2.58% 89.68% NA
Indica III  913 26.50% 2.70% 0.77% 69.99% NA
Indica Intermediate  786 14.10% 1.80% 1.65% 82.44% NA
Temperate Japonica  767 83.60% 13.80% 0.00% 2.61% NA
Tropical Japonica  504 1.80% 93.70% 0.60% 3.97% NA
Japonica Intermediate  241 31.10% 65.10% 0.41% 3.32% NA
VI/Aromatic  96 74.00% 22.90% 0.00% 3.12% NA
Intermediate  90 34.40% 21.10% 4.44% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0104343872 A -> G LOC_Os01g08710.1 synonymous_variant ; p.Ala276Ala; LOW synonymous_codon Average:84.19; most accessible tissue: Minghui63 root, score: 90.092 N N N N
vg0104343872 A -> DEL LOC_Os01g08710.1 N frameshift_variant Average:84.19; most accessible tissue: Minghui63 root, score: 90.092 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)
vg0104343872 A G 0.01 0.0 0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104343872 NA 4.56E-06 mr1300 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
vg0104343872 NA 7.46E-07 mr1310 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
vg0104343872 NA 1.38E-08 mr1354 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
vg0104343872 NA 2.64E-14 mr1449 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
vg0104343872 NA 5.27E-06 mr1565 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
vg0104343872 NA 8.26E-06 mr1657 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
vg0104343872 NA 1.10E-08 mr1806 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
vg0104343872 NA 9.85E-08 mr1310_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
vg0104343872 NA 3.40E-08 mr1335_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
vg0104343872 NA 2.77E-15 mr1354_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
vg0104343872 NA 4.82E-07 mr1354_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
vg0104343872 NA 2.98E-08 mr1582_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
vg0104343872 NA 3.22E-06 mr1582_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
vg0104343872 NA 9.70E-10 mr1646_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
vg0104343872 NA 7.04E-30 mr1699_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
vg0104343872 NA 1.99E-10 mr1761_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
vg0104343872 NA 8.33E-10 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
vg0104343872 NA 1.01E-13 mr1864_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
vg0104343872 NA 1.32E-20 mr1871_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
vg0104343872 NA 2.84E-06 mr1966_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