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Detailed information for vg0222615084:

Variant ID: vg0222615084 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22615084
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGTCCAAGCCAAGAAGGAGACTGGAGCAAAGCCAGGGTCCTGCTTCAACTGTGGCGAGCATGGCCACTTTGCTGACAAGTGCCCGAAGCCAAGGCGTG[C/A,T]
CGAGCCAAGGTTTGCCCAAGCTCGTATCAACCACGCATCCGTAGAAGAGGCGCAAGCAGCACCAGAGGTCGTACTGGGTACGTTTCCTGTCAACTCAATT

Reverse complement sequence

AATTGAGTTGACAGGAAACGTACCCAGTACGACCTCTGGTGCTGCTTGCGCCTCTTCTACGGATGCGTGGTTGATACGAGCTTGGGCAAACCTTGGCTCG[G/T,A]
CACGCCTTGGCTTCGGGCACTTGTCAGCAAAGTGGCCATGCTCGCCACAGTTGAAGCAGGACCCTGGCTTTGCTCCAGTCTCCTTCTTGGCTTGGACTGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 4.20% 4.61% 0.51% NA
All Indica  2759 85.30% 6.80% 7.07% 0.83% NA
All Japonica  1512 99.30% 0.40% 0.33% 0.00% NA
Aus  269 94.10% 0.00% 5.95% 0.00% NA
Indica I  595 96.60% 0.00% 3.36% 0.00% NA
Indica II  465 62.40% 18.10% 17.42% 2.15% NA
Indica III  913 92.40% 4.30% 3.07% 0.22% NA
Indica Intermediate  786 81.90% 8.30% 8.40% 1.40% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 0.80% 0.79% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 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
vg0222615084 C -> A LOC_Os02g37460.1 missense_variant ; p.Ala248Asp; MODERATE nonsynonymous_codon ; A248D Average:64.599; most accessible tissue: Minghui63 young leaf, score: 82.907 probably damaging 2.203 DELETERIOUS 0.01
vg0222615084 C -> T LOC_Os02g37460.1 missense_variant ; p.Ala248Val; MODERATE N Average:64.599; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg0222615084 C -> T LOC_Os02g37450.1 upstream_gene_variant ; 3001.0bp to feature; MODIFIER N Average:64.599; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg0222615084 C -> T LOC_Os02g37470.1 upstream_gene_variant ; 2419.0bp to feature; MODIFIER N Average:64.599; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg0222615084 C -> DEL LOC_Os02g37460.1 N frameshift_variant Average:64.599; most accessible tissue: Minghui63 young leaf, score: 82.907 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)
vg0222615084 C A 0.0 -0.01 -0.01 0.0 0.0 0.0
vg0222615084 C T 0.0 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222615084 NA 4.10E-08 mr1069 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
vg0222615084 NA 4.36E-07 mr1072 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
vg0222615084 NA 6.80E-07 mr1074 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
vg0222615084 NA 6.15E-07 mr1077 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
vg0222615084 NA 2.26E-06 mr1095 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
vg0222615084 NA 3.21E-07 mr1098 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
vg0222615084 NA 8.20E-07 mr1099 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
vg0222615084 4.45E-06 3.95E-07 mr1101 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
vg0222615084 NA 4.73E-06 mr1149 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
vg0222615084 NA 7.50E-08 mr1150 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
vg0222615084 NA 3.18E-06 mr1180 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
vg0222615084 NA 4.96E-06 mr1202 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
vg0222615084 NA 8.31E-07 mr1441 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
vg0222615084 4.59E-06 4.64E-07 mr1589 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
vg0222615084 NA 6.38E-06 mr1592 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
vg0222615084 9.76E-06 6.59E-07 mr1868 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
vg0222615084 NA 1.64E-08 mr1877 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
vg0222615084 NA 3.21E-08 mr1911 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
vg0222615084 NA 1.90E-11 mr1918 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
vg0222615084 1.66E-07 2.90E-11 mr1929 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
vg0222615084 NA 9.25E-07 mr1962 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
vg0222615084 NA 3.12E-06 mr1074_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
vg0222615084 NA 4.05E-06 mr1095_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
vg0222615084 NA 6.16E-08 mr1098_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
vg0222615084 NA 7.02E-08 mr1099_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
vg0222615084 3.77E-06 1.99E-06 mr1146_2 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
vg0222615084 NA 1.53E-07 mr1149_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
vg0222615084 NA 9.95E-11 mr1150_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
vg0222615084 NA 5.95E-07 mr1222_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
vg0222615084 NA 6.64E-08 mr1441_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
vg0222615084 NA 4.23E-08 mr1861_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
vg0222615084 NA 7.07E-06 mr1871_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
vg0222615084 NA 2.65E-08 mr1918_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
vg0222615084 8.44E-07 6.18E-09 mr1929_2 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