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Detailed information for vg0907179681:

Variant ID: vg0907179681 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7179681
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, T: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTGCGGATGCCTCCGCAGACAACGAGGACACCACTAACGCTGCTGCAATGTGCGACGAGCTGGAGGAGACCAGAACATCGTTTCAAGGGGAATACAAT[T/G]
ATGTGGATTGGTGCTTAGTGTGGTGGTGATCGATAATTCCCGAGATGTTGTAAGACGACACATAAAAGAAAACGATGGGGGCAGGTGAGCAGTTGGCGAT

Reverse complement sequence

ATCGCCAACTGCTCACCTGCCCCCATCGTTTTCTTTTATGTGTCGTCTTACAACATCTCGGGAATTATCGATCACCACCACACTAAGCACCAATCCACAT[A/C]
ATTGTATTCCCCTTGAAACGATGTTCTGGTCTCCTCCAGCTCGTCGCACATTGCAGCAGCGTTAGTGGTGTCCTCGTTGTCTGCGGAGGCATCCGCAAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.50% 10.50% 4.00% 0.00% NA
All Indica  2759 98.00% 0.70% 1.34% 0.00% NA
All Japonica  1512 62.60% 31.20% 6.22% 0.00% NA
Aus  269 81.40% 0.00% 18.59% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 97.20% 0.70% 2.19% 0.00% NA
Indica Intermediate  786 96.80% 1.10% 2.04% 0.00% NA
Temperate Japonica  767 38.50% 53.10% 8.47% 0.00% NA
Tropical Japonica  504 92.70% 3.40% 3.97% 0.00% NA
Japonica Intermediate  241 76.80% 19.50% 3.73% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 3.12% 0.00% NA
Intermediate  90 85.60% 8.90% 5.56% 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
vg0907179681 T -> G LOC_Os09g12520.1 upstream_gene_variant ; 2470.0bp to feature; MODIFIER silent_mutation Average:85.753; most accessible tissue: Callus, score: 93.245 N N N N
vg0907179681 T -> G LOC_Os09g12530.1 upstream_gene_variant ; 282.0bp to feature; MODIFIER silent_mutation Average:85.753; most accessible tissue: Callus, score: 93.245 N N N N
vg0907179681 T -> G LOC_Os09g12520-LOC_Os09g12530 intergenic_region ; MODIFIER silent_mutation Average:85.753; most accessible tissue: Callus, score: 93.245 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)
vg0907179681 T G -0.02 -0.01 -0.02 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907179681 NA 1.00E-14 Spikelet_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
vg0907179681 NA 6.00E-06 mr1002 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
vg0907179681 NA 8.11E-09 mr1137 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
vg0907179681 NA 2.71E-07 mr1252 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
vg0907179681 NA 4.25E-06 mr1330 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
vg0907179681 NA 2.12E-07 mr1763 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
vg0907179681 4.86E-06 NA mr1789 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
vg0907179681 NA 1.34E-06 mr1977 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
vg0907179681 NA 8.81E-10 mr1002_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
vg0907179681 NA 1.30E-07 mr1010_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
vg0907179681 NA 6.15E-11 mr1011_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
vg0907179681 NA 3.58E-07 mr1011_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
vg0907179681 NA 8.39E-14 mr1182_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
vg0907179681 NA 1.29E-06 mr1182_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
vg0907179681 NA 9.24E-11 mr1282_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
vg0907179681 NA 1.09E-06 mr1330_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
vg0907179681 NA 3.10E-07 mr1880_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