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Detailed information for vg0102754939:

Variant ID: vg0102754939 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2754939
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTGTCGAGGTTCGAGCTTCCCCATGGCGATTGACTGGCGGCGTGGTGCCGGTGCGGTGGCCATGCGTCGAAGGTTTTCGCTGGTGGTGGCTGCGGAGC[G/A,T]
TGTAGGAGTTCAGTTCTTGGGAGAGACAAATTTTGGGCGAAAGCTCTGCCTTCGAGCCGGCAACAACGACGCCTGTGGGTGCCGTTTTTTCCTCTTGGGG

Reverse complement sequence

CCCCAAGAGGAAAAAACGGCACCCACAGGCGTCGTTGTTGCCGGCTCGAAGGCAGAGCTTTCGCCCAAAATTTGTCTCTCCCAAGAACTGAACTCCTACA[C/T,A]
GCTCCGCAGCCACCACCAGCGAAAACCTTCGACGCATGGCCACCGCACCGGCACCACGCCGCCAGTCAATCGCCATGGGGAAGCTCGAACCTCGACACAC

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 81.80% 7.20% 7.58% 3.36% T: 0.04%
All Indica  2759 97.90% 0.10% 1.74% 0.14% T: 0.04%
All Japonica  1512 49.40% 21.40% 18.98% 10.19% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 95.80% 0.00% 3.53% 0.67% NA
Indica II  465 99.10% 0.20% 0.65% 0.00% NA
Indica III  913 98.40% 0.20% 1.31% 0.00% T: 0.11%
Indica Intermediate  786 98.30% 0.10% 1.53% 0.00% NA
Temperate Japonica  767 39.60% 34.90% 16.30% 9.13% NA
Tropical Japonica  504 69.60% 0.80% 20.83% 8.73% NA
Japonica Intermediate  241 38.20% 21.60% 23.65% 16.60% NA
VI/Aromatic  96 66.70% 10.40% 21.88% 0.00% T: 1.04%
Intermediate  90 93.30% 4.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0102754939 G -> T LOC_Os01g05770.1 missense_variant ; p.Arg315Leu; MODERATE nonsynonymous_codon ; R315L Average:81.989; most accessible tissue: Minghui63 flag leaf, score: 94.034 unknown unknown DELETERIOUS 0.00
vg0102754939 G -> A LOC_Os01g05770.1 missense_variant ; p.Arg315His; MODERATE nonsynonymous_codon ; R315H Average:81.989; most accessible tissue: Minghui63 flag leaf, score: 94.034 unknown unknown DELETERIOUS 0.00
vg0102754939 G -> DEL LOC_Os01g05770.1 N frameshift_variant Average:81.989; most accessible tissue: Minghui63 flag leaf, score: 94.034 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)
vg0102754939 G A -0.04 -0.02 -0.02 -0.06 -0.06 -0.07
vg0102754939 G T -0.06 -0.04 -0.04 -0.1 -0.1 -0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102754939 NA 1.92E-17 Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0102754939 NA 7.91E-06 mr1424 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
vg0102754939 NA 3.71E-07 mr1829 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
vg0102754939 NA 2.58E-07 mr1916 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
vg0102754939 NA 2.46E-07 mr1042_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
vg0102754939 NA 6.87E-07 mr1045_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
vg0102754939 NA 1.06E-06 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
vg0102754939 NA 1.06E-08 mr1471_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
vg0102754939 NA 1.93E-07 mr1502_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
vg0102754939 2.80E-06 1.67E-09 mr1567_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
vg0102754939 NA 1.42E-06 mr1567_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
vg0102754939 NA 9.96E-08 mr1680_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
vg0102754939 1.28E-06 NA mr1806_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
vg0102754939 NA 2.73E-16 mr1827_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
vg0102754939 NA 1.22E-11 mr1829_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
vg0102754939 NA 3.06E-16 mr1842_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
vg0102754939 NA 4.41E-08 mr1871_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
vg0102754939 NA 3.13E-18 mr1902_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
vg0102754939 NA 3.14E-07 mr1952_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