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Detailed information for vg1018295419:

Variant ID: vg1018295419 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18295419
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCACCTCCATGTCCGCGGCCCTTGGCGGAGATTCTGCAGGCTTCCATACCTCGTGGCCACCGACGAGCTGTGTCCGGCACCGCAGCTCGTAGGCCCGC[G/A]
TCTCGAAGTTCCAGCAGTCGAGATGGACCGCCAAGTGCGCGCCGGTCGCCGCGTCGTAGCCGAGCGCCATGACGCCGTCGAACACTCTGTCGTCGTAGTC

Reverse complement sequence

GACTACGACGACAGAGTGTTCGACGGCGTCATGGCGCTCGGCTACGACGCGGCGACCGGCGCGCACTTGGCGGTCCATCTCGACTGCTGGAACTTCGAGA[C/T]
GCGGGCCTACGAGCTGCGGTGCCGGACACAGCTCGTCGGTGGCCACGAGGTATGGAAGCCTGCAGAATCTCCGCCAAGGGCCGCGGACATGGAGGTGCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.10% 35.60% 1.23% 1.10% NA
All Indica  2759 43.40% 52.80% 2.03% 1.74% NA
All Japonica  1512 89.70% 10.10% 0.00% 0.13% NA
Aus  269 83.30% 16.70% 0.00% 0.00% NA
Indica I  595 8.10% 89.20% 2.69% 0.00% NA
Indica II  465 65.20% 32.70% 1.29% 0.86% NA
Indica III  913 51.20% 42.10% 2.52% 4.27% NA
Indica Intermediate  786 48.20% 49.70% 1.40% 0.64% NA
Temperate Japonica  767 97.40% 2.50% 0.00% 0.13% NA
Tropical Japonica  504 76.00% 23.80% 0.00% 0.20% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 68.90% 27.80% 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
vg1018295419 G -> A LOC_Os10g34300.1 missense_variant ; p.Thr519Met; MODERATE nonsynonymous_codon ; T519M Average:88.959; most accessible tissue: Zhenshan97 panicle, score: 97.277 unknown unknown DELETERIOUS 0.03
vg1018295419 G -> DEL LOC_Os10g34300.1 N frameshift_variant Average:88.959; most accessible tissue: Zhenshan97 panicle, score: 97.277 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)
vg1018295419 G A -0.05 -0.04 -0.03 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018295419 NA 2.55E-11 mr1784 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
vg1018295419 NA 1.30E-06 mr1805 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
vg1018295419 NA 7.32E-06 mr1817 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
vg1018295419 NA 1.81E-08 mr1862 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
vg1018295419 NA 1.79E-08 mr1942 Ind_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
vg1018295419 NA 3.20E-06 mr1039_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
vg1018295419 NA 9.55E-11 mr1050_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
vg1018295419 NA 2.17E-08 mr1272_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
vg1018295419 NA 1.06E-08 mr1558_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
vg1018295419 NA 1.73E-08 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
vg1018295419 NA 1.14E-06 mr1632_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
vg1018295419 NA 8.96E-10 mr1835_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
vg1018295419 NA 2.32E-14 mr1904_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
vg1018295419 NA 2.31E-07 mr1904_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
vg1018295419 NA 4.47E-07 mr1910_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
vg1018295419 NA 2.80E-06 mr1942_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