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Detailed information for vg1005360762:

Variant ID: vg1005360762 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5360762
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: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCCGTCCATCCCCAGGCCCCGAAGCTCGTCGCGGGCATCAGAGAGAAGAACCCTAACCCTAACTAGGGTTAGGGTTATGGCGATGCAGCGAAGAATT[G/A]
CTCAAGGTAGCGAGGACATGTCCCAAGGTAGTTCCTTTCGTGCTCCCGGGCGCCAACTCTCTCGTTTTCTTCTTGGTCCCAGTGGACTTCCTCTTGTGAA

Reverse complement sequence

TTCACAAGAGGAAGTCCACTGGGACCAAGAAGAAAACGAGAGAGTTGGCGCCCGGGAGCACGAAAGGAACTACCTTGGGACATGTCCTCGCTACCTTGAG[C/T]
AATTCTTCGCTGCATCGCCATAACCCTAACCCTAGTTAGGGTTAGGGTTCTTCTCTCTGATGCCCGCGACGAGCTTCGGGGCCTGGGGATGGACGGCGGC

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 64.40% 8.80% 2.20% 24.61% NA
All Indica  2759 64.90% 14.00% 2.57% 18.52% NA
All Japonica  1512 63.00% 0.90% 1.72% 34.39% NA
Aus  269 51.30% 4.10% 1.86% 42.75% NA
Indica I  595 73.40% 7.60% 3.36% 15.63% NA
Indica II  465 52.50% 25.20% 3.66% 18.71% NA
Indica III  913 61.90% 13.50% 2.08% 22.56% NA
Indica Intermediate  786 69.30% 12.80% 1.91% 15.90% NA
Temperate Japonica  767 74.20% 0.50% 1.30% 23.99% NA
Tropical Japonica  504 48.60% 0.60% 2.58% 48.21% NA
Japonica Intermediate  241 57.70% 2.50% 1.24% 38.59% NA
VI/Aromatic  96 90.60% 1.00% 0.00% 8.33% NA
Intermediate  90 81.10% 6.70% 2.22% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005360762 G -> A LOC_Os10g09890.1 missense_variant ; p.Ala8Thr; MODERATE nonsynonymous_codon ; A8T Average:47.265; most accessible tissue: Zhenshan97 panicle, score: 80.486 unknown unknown TOLERATED 0.24
vg1005360762 G -> DEL LOC_Os10g09890.1 N frameshift_variant Average:47.265; most accessible tissue: Zhenshan97 panicle, score: 80.486 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)
vg1005360762 G A 0.04 0.02 0.01 0.03 0.03 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005360762 6.11E-06 8.39E-07 mr1254 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
vg1005360762 NA 1.87E-08 mr1855 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
vg1005360762 6.66E-06 6.66E-06 mr1863 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
vg1005360762 NA 4.92E-08 mr1855_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