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Detailed information for vg1016393079:

Variant ID: vg1016393079 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16393079
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, G: 0.11, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGATGAATCCATGGATGATGCGCGCGGAGTTGATGGACCAGAGCAACCAACCGGGGACCTTGAGAAGCATGCTGACACTATGGGAGCGAAGGATGTGG[G/C]
CGGTCCAGAAGGAGGACATGAGATCGAACAGCGGGGTCTGCTTCATGGCGATGCCGGCGGGGCGGCCGATCTTGACGCTGTAGCGGAGGGTGACCAGCAG

Reverse complement sequence

CTGCTGGTCACCCTCCGCTACAGCGTCAAGATCGGCCGCCCCGCCGGCATCGCCATGAAGCAGACCCCGCTGTTCGATCTCATGTCCTCCTTCTGGACCG[C/G]
CCACATCCTTCGCTCCCATAGTGTCAGCATGCTTCTCAAGGTCCCCGGTTGGTTGCTCTGGTCCATCAACTCCGCGCGCATCATCCATGGATTCATCTCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.10% 31.90% 0.28% 2.77% NA
All Indica  2759 94.60% 1.50% 0.36% 3.48% NA
All Japonica  1512 5.00% 94.40% 0.13% 0.46% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 89.70% 1.20% 0.34% 8.74% NA
Indica II  465 92.50% 3.00% 0.86% 3.66% NA
Indica III  913 98.50% 0.10% 0.00% 1.42% NA
Indica Intermediate  786 95.20% 2.50% 0.51% 1.78% NA
Temperate Japonica  767 1.00% 98.70% 0.00% 0.26% NA
Tropical Japonica  504 5.60% 93.50% 0.40% 0.60% NA
Japonica Intermediate  241 16.20% 83.00% 0.00% 0.83% NA
VI/Aromatic  96 75.00% 0.00% 0.00% 25.00% NA
Intermediate  90 55.60% 38.90% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1016393079 G -> C LOC_Os10g31250.1 missense_variant ; p.Ala116Gly; MODERATE nonsynonymous_codon ; A116G Average:77.119; most accessible tissue: Minghui63 panicle, score: 91.919 benign -0.2 TOLERATED 0.06
vg1016393079 G -> DEL LOC_Os10g31250.1 N frameshift_variant Average:77.119; most accessible tissue: Minghui63 panicle, score: 91.919 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)
vg1016393079 G C -0.02 0.0 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016393079 NA 3.62E-13 mr1010 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
vg1016393079 NA 1.88E-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
vg1016393079 NA 7.38E-08 mr1359 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
vg1016393079 NA 1.74E-31 mr1448 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
vg1016393079 NA 1.90E-36 mr1486 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
vg1016393079 NA 3.38E-06 mr1530 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
vg1016393079 NA 1.18E-20 mr1541 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
vg1016393079 NA 7.57E-09 mr1637 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
vg1016393079 NA 3.01E-10 mr1663 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
vg1016393079 NA 3.34E-07 mr1671 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
vg1016393079 NA 3.34E-25 mr1689 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
vg1016393079 NA 5.76E-09 mr1691 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
vg1016393079 NA 1.51E-06 mr1704 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
vg1016393079 NA 3.00E-10 mr1712 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
vg1016393079 NA 5.92E-13 mr1740 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
vg1016393079 NA 1.62E-06 mr1815 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
vg1016393079 NA 4.92E-06 mr1837 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
vg1016393079 NA 1.02E-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
vg1016393079 NA 2.05E-52 mr1991_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