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Detailed information for vg1003801826:

Variant ID: vg1003801826 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3801826
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.10, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATGGGGACAACATGATCTCCAGGGGCAAGATCCTCCACACCCTCTCCCACGCTCTCCACCACCCTGTTTTTTTAGTTGCATATTGCTATCAGGTGTT[G/T]
TATAAAAATGGTAACGTCTTTAATGTGCCAAAAATATACTCTTTAGGATGAGTGCTTTTACTATGACAAGATGTATTCAGTTTTGTGAAAACATGCAAAT

Reverse complement sequence

ATTTGCATGTTTTCACAAAACTGAATACATCTTGTCATAGTAAAAGCACTCATCCTAAAGAGTATATTTTTGGCACATTAAAGACGTTACCATTTTTATA[C/A]
AACACCTGATAGCAATATGCAACTAAAAAAACAGGGTGGTGGAGAGCGTGGGAGAGGGTGTGGAGGATCTTGCCCCTGGAGATCATGTTGTCCCCATCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.80% 8.20% 0.04% 0.00% NA
All Indica  2759 95.80% 4.20% 0.04% 0.00% NA
All Japonica  1512 93.40% 6.60% 0.00% 0.00% NA
Aus  269 43.90% 56.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 92.80% 7.10% 0.11% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 94.70% 5.30% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg1003801826 G -> T LOC_Os10g07229.1 intron_variant ; MODIFIER silent_mutation Average:82.435; most accessible tissue: Zhenshan97 root, score: 95.724 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)
vg1003801826 G T -0.02 -0.04 -0.04 -0.02 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003801826 NA 2.04E-06 mr1349 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
vg1003801826 NA 5.41E-08 mr1669 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
vg1003801826 4.52E-06 NA mr1691_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