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Detailed information for vg0102820770:

Variant ID: vg0102820770 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2820770
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, C: 0.33, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCTTCTTCTCCGCCTTGGGCGCCATGGATGCCGCTCTCTTCTTCTCGGGGAAGGGAAAGGGGAGACGAAAATTTGGGGGAATTCGGTTGCGAGTTGTG[G/C]
AGTTGAAGGGGAGGCGGCGGCGATGGTATTAAAGGAGGGGAGAGGTGGGCGCTGATTGGCGGAGGGGGTGCGCCGCGGATCGATGACGTGGAGGAGCATG

Reverse complement sequence

CATGCTCCTCCACGTCATCGATCCGCGGCGCACCCCCTCCGCCAATCAGCGCCCACCTCTCCCCTCCTTTAATACCATCGCCGCCGCCTCCCCTTCAACT[C/G]
CACAACTCGCAACCGAATTCCCCCAAATTTTCGTCTCCCCTTTCCCTTCCCCGAGAAGAAGAGAGCGGCATCCATGGCGCCCAAGGCGGAGAAGAAGCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 41.20% 0.87% 4.02% NA
All Indica  2759 55.40% 42.90% 0.94% 0.76% NA
All Japonica  1512 55.40% 44.40% 0.13% 0.07% NA
Aus  269 35.70% 3.00% 2.97% 58.36% NA
Indica I  595 74.50% 25.20% 0.34% 0.00% NA
Indica II  465 27.30% 69.70% 1.08% 1.94% NA
Indica III  913 61.00% 37.60% 0.99% 0.44% NA
Indica Intermediate  786 51.00% 46.70% 1.27% 1.02% NA
Temperate Japonica  767 25.00% 74.80% 0.13% 0.00% NA
Tropical Japonica  504 96.20% 3.40% 0.20% 0.20% NA
Japonica Intermediate  241 66.80% 33.20% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 60.40% 0.00% 7.29% NA
Intermediate  90 60.00% 30.00% 5.56% 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
vg0102820770 G -> DEL N N silent_mutation Average:99.047; most accessible tissue: Callus, score: 99.704 N N N N
vg0102820770 G -> C LOC_Os01g05880.1 upstream_gene_variant ; 4369.0bp to feature; MODIFIER silent_mutation Average:99.047; most accessible tissue: Callus, score: 99.704 N N N N
vg0102820770 G -> C LOC_Os01g05890.1 upstream_gene_variant ; 1873.0bp to feature; MODIFIER silent_mutation Average:99.047; most accessible tissue: Callus, score: 99.704 N N N N
vg0102820770 G -> C LOC_Os01g05900.1 intron_variant ; MODIFIER silent_mutation Average:99.047; most accessible tissue: Callus, score: 99.704 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)
vg0102820770 G C 0.0 -0.02 -0.02 -0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102820770 NA 9.03E-08 mr1174 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
vg0102820770 NA 3.86E-10 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
vg0102820770 NA 8.81E-06 mr1063_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
vg0102820770 NA 9.77E-06 mr1127_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
vg0102820770 NA 3.12E-07 mr1169_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
vg0102820770 NA 1.28E-09 mr1174_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
vg0102820770 NA 1.04E-06 mr1347_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
vg0102820770 NA 9.81E-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
vg0102820770 NA 6.71E-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
vg0102820770 NA 6.98E-12 mr1580_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
vg0102820770 NA 9.39E-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
vg0102820770 NA 1.16E-07 mr1748_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
vg0102820770 NA 1.56E-10 mr1825_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
vg0102820770 NA 1.23E-15 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
vg0102820770 NA 1.06E-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
vg0102820770 NA 2.61E-17 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