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Detailed information for vg0920177153:

Variant ID: vg0920177153 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20177153
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTTTATAAAGGGAGTACTACTCTACTACTCCTACTCCTAATTAAGAGTGTTGGAGTGTTTATTAATGACCAGAACACAATCCTCGTGTGTCGTAC[G/A]
AGTACAGCATGACGAACTGGGACGCATGGACGGTGACAGGTGATTGGCACTGTTTGCTGCTGACACGCAGCAATAATGTGTTCGGCTCGTGTTCGAGAAC

Reverse complement sequence

GTTCTCGAACACGAGCCGAACACATTATTGCTGCGTGTCAGCAGCAAACAGTGCCAATCACCTGTCACCGTCCATGCGTCCCAGTTCGTCATGCTGTACT[C/T]
GTACGACACACGAGGATTGTGTTCTGGTCATTAATAAACACTCCAACACTCTTAATTAGGAGTAGGAGTAGTAGAGTAGTACTCCCTTTATAAAAAAAAA

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 89.70% 10.30% 0.00% 0.00% NA
All Indica  2759 94.40% 5.60% 0.00% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 3.70% 96.30% 0.00% 0.00% NA
Indica I  595 92.90% 7.10% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 94.20% 5.80% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 7.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 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
vg0920177153 G -> A LOC_Os09g34170.1 upstream_gene_variant ; 4520.0bp to feature; MODIFIER silent_mutation Average:96.583; most accessible tissue: Minghui63 root, score: 98.864 N N N N
vg0920177153 G -> A LOC_Os09g34180.1 upstream_gene_variant ; 2561.0bp to feature; MODIFIER silent_mutation Average:96.583; most accessible tissue: Minghui63 root, score: 98.864 N N N N
vg0920177153 G -> A LOC_Os09g34170-LOC_Os09g34180 intergenic_region ; MODIFIER silent_mutation Average:96.583; most accessible tissue: Minghui63 root, score: 98.864 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)
vg0920177153 G A -0.05 -0.02 -0.01 -0.01 -0.01 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920177153 NA 3.53E-06 Spikelet_length Ind_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
vg0920177153 NA 6.80E-07 mr1177 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
vg0920177153 4.09E-08 NA mr1261 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
vg0920177153 NA 1.60E-06 mr1261 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
vg0920177153 NA 2.23E-06 mr1510 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
vg0920177153 NA 1.13E-07 mr1707 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
vg0920177153 NA 5.49E-09 mr1739 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
vg0920177153 NA 2.52E-07 mr1740 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
vg0920177153 NA 4.74E-06 mr1806 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
vg0920177153 NA 2.91E-09 mr1739_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
vg0920177153 NA 5.57E-07 mr1834_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