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Detailed information for vg0105833744:

Variant ID: vg0105833744 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5833744
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAGGCGGGCGCCGAGCTTGGTGGCGAGGACGTGGCTGAGGGGCATCAGCTCAGGGGTCTCGTCGGTGGCGTAGCCGAACATGTGGCCCTGGTCGCCGG[C/T]
GCCGATCTCCTCGGGGTGCTTGGTGAAGTGGCCGTGCACGCCCTGGGCAATGTCGGGCGACTGCTGCTCGATGTTGACGAGCACCTTGCAGCGGTCGGCG

Reverse complement sequence

CGCCGACCGCTGCAAGGTGCTCGTCAACATCGAGCAGCAGTCGCCCGACATTGCCCAGGGCGTGCACGGCCACTTCACCAAGCACCCCGAGGAGATCGGC[G/A]
CCGGCGACCAGGGCCACATGTTCGGCTACGCCACCGACGAGACCCCTGAGCTGATGCCCCTCAGCCACGTCCTCGCCACCAAGCTCGGCGCCCGCCTCAC

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 92.90% 2.50% 0.61% 3.94% NA
All Indica  2759 95.10% 0.10% 0.29% 4.46% NA
All Japonica  1512 89.40% 7.40% 0.99% 2.18% NA
Aus  269 87.40% 0.40% 1.86% 10.41% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 93.30% 0.00% 0.86% 5.81% NA
Indica III  913 94.00% 0.10% 0.11% 5.81% NA
Indica Intermediate  786 94.00% 0.30% 0.38% 5.34% NA
Temperate Japonica  767 97.40% 2.10% 0.13% 0.39% NA
Tropical Japonica  504 94.00% 3.00% 1.59% 1.39% NA
Japonica Intermediate  241 54.40% 33.60% 2.49% 9.54% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0105833744 C -> T LOC_Os01g10940.1 missense_variant ; p.Ala122Thr; MODERATE nonsynonymous_codon ; A122T Average:85.82; most accessible tissue: Minghui63 flag leaf, score: 94.147 possibly damaging 1.571 DELETERIOUS 0.00
vg0105833744 C -> DEL LOC_Os01g10940.1 N frameshift_variant Average:85.82; most accessible tissue: Minghui63 flag leaf, score: 94.147 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)
vg0105833744 C T 0.01 0.0 0.01 0.0 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105833744 NA 9.01E-08 mr1117 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
vg0105833744 NA 5.46E-07 mr1118 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
vg0105833744 NA 1.43E-06 mr1119 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
vg0105833744 NA 9.37E-08 mr1123 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
vg0105833744 NA 5.68E-07 mr1242 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
vg0105833744 NA 2.52E-06 mr1247 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
vg0105833744 NA 4.68E-07 mr1496 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
vg0105833744 NA 2.01E-06 mr1113_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
vg0105833744 NA 1.70E-07 mr1114_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
vg0105833744 8.71E-06 7.64E-10 mr1117_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
vg0105833744 1.42E-06 1.58E-10 mr1118_2 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
vg0105833744 NA 9.80E-09 mr1119_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
vg0105833744 NA 9.77E-07 mr1120_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
vg0105833744 NA 5.23E-08 mr1123_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
vg0105833744 NA 5.36E-10 mr1240_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
vg0105833744 NA 2.09E-08 mr1242_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
vg0105833744 NA 1.80E-06 mr1247_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
vg0105833744 NA 4.58E-08 mr1495_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
vg0105833744 5.78E-07 6.59E-12 mr1496_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