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Detailed information for vg0715690956:

Variant ID: vg0715690956 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15690956
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACAGAGAGGAGGAAGGTACAGCCGGTGAAGAAATTGACCCATCACCGCTGTCCGCGATGCCGAGCAGCAGGATTCAGGCGCGGGGCCCCAAATTCGAC[G/A]
GCGGCTCCACAGGATGCACCTGCATCGCCACCACCATCGCCGGGTCCTAGGTCCCAGCCGCCCATCACCGTCGTTGCCGTCAGAGACGTCGGGAAAAGCA

Reverse complement sequence

TGCTTTTCCCGACGTCTCTGACGGCAACGACGGTGATGGGCGGCTGGGACCTAGGACCCGGCGATGGTGGTGGCGATGCAGGTGCATCCTGTGGAGCCGC[C/T]
GTCGAATTTGGGGCCCCGCGCCTGAATCCTGCTGCTCGGCATCGCGGACAGCGGTGATGGGTCAATTTCTTCACCGGCTGTACCTTCCTCCTCTCTGTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.00% 42.70% 0.21% 3.11% NA
All Indica  2759 82.00% 15.70% 0.25% 2.07% NA
All Japonica  1512 0.80% 93.50% 0.00% 5.69% NA
Aus  269 86.60% 12.30% 0.00% 1.12% NA
Indica I  595 97.00% 1.50% 0.34% 1.18% NA
Indica II  465 93.30% 5.60% 0.22% 0.86% NA
Indica III  913 72.30% 27.30% 0.11% 0.33% NA
Indica Intermediate  786 75.20% 19.00% 0.38% 5.47% NA
Temperate Japonica  767 0.90% 89.00% 0.00% 10.04% NA
Tropical Japonica  504 0.40% 98.00% 0.00% 1.59% NA
Japonica Intermediate  241 1.20% 98.30% 0.00% 0.41% NA
VI/Aromatic  96 7.30% 91.70% 1.04% 0.00% NA
Intermediate  90 41.10% 55.60% 2.22% 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
vg0715690956 G -> DEL LOC_Os07g27070.1 N frameshift_variant Average:72.956; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg0715690956 G -> A LOC_Os07g27070.1 synonymous_variant ; p.Thr1172Thr; LOW synonymous_codon Average:72.956; most accessible tissue: Zhenshan97 young leaf, score: 88.995 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)
vg0715690956 G A -0.02 -0.01 -0.01 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715690956 NA 5.18E-06 Awn_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
vg0715690956 NA 1.37E-06 mr1042 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
vg0715690956 NA 2.31E-06 mr1043 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
vg0715690956 NA 1.38E-28 mr1075 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
vg0715690956 NA 9.48E-24 mr1155 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
vg0715690956 NA 1.22E-07 mr1155 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
vg0715690956 NA 1.82E-07 mr1162 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
vg0715690956 NA 4.49E-27 mr1181 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
vg0715690956 NA 7.81E-08 mr1181 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
vg0715690956 NA 2.18E-11 mr1281 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
vg0715690956 NA 6.37E-06 mr1479 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
vg0715690956 NA 2.18E-19 mr1566 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
vg0715690956 NA 1.06E-08 mr1595 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
vg0715690956 NA 1.02E-11 mr1630 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
vg0715690956 2.16E-06 2.05E-07 mr1768 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
vg0715690956 NA 7.23E-23 mr1888 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
vg0715690956 NA 3.16E-09 mr1915 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
vg0715690956 NA 1.16E-09 mr1945 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
vg0715690956 NA 3.46E-33 mr1841_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
vg0715690956 NA 2.17E-06 mr1915_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
vg0715690956 NA 9.25E-19 mr1945_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
vg0715690956 NA 2.04E-06 mr1996_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