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Detailed information for vg0228803563:

Variant ID: vg0228803563 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28803563
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


ATACCGGACAGGTCGGCGATGGACATGGACATGGCGCACTACCTGCTCACGGAGCCCAAGAAGGACAAGGAGAACGCGGCGGCGTCCCCGTCCAAGGAGG[T/C]
GTACCGGAGGCTGCTCGCCGAGAAGCTGCTCAACAACCGGACACGGATCCTCGCCTTCCGGAACAAGCCACCGGAGCCCGAGAACGTCTCTGCCGCGGAT

Reverse complement sequence

ATCCGCGGCAGAGACGTTCTCGGGCTCCGGTGGCTTGTTCCGGAAGGCGAGGATCCGTGTCCGGTTGTTGAGCAGCTTCTCGGCGAGCAGCCTCCGGTAC[A/G]
CCTCCTTGGACGGGGACGCCGCCGCGTTCTCCTTGTCCTTCTTGGGCTCCGTGAGCAGGTAGTGCGCCATGTCCATGTCCATCGCCGACCTGTCCGGTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.80% 40.80% 0.02% 0.42% NA
All Indica  2759 84.70% 14.70% 0.04% 0.62% NA
All Japonica  1512 15.10% 84.80% 0.00% 0.07% NA
Aus  269 52.40% 47.60% 0.00% 0.00% NA
Indica I  595 91.90% 7.40% 0.00% 0.67% NA
Indica II  465 92.90% 6.00% 0.22% 0.86% NA
Indica III  913 82.40% 17.30% 0.00% 0.33% NA
Indica Intermediate  786 77.00% 22.30% 0.00% 0.76% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 43.70% 56.30% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.50% 0.00% 0.41% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 41.10% 56.70% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0228803563 T -> DEL LOC_Os02g47180.1 N frameshift_variant Average:91.787; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0228803563 T -> DEL LOC_Os02g47180.2 N frameshift_variant Average:91.787; most accessible tissue: Minghui63 flower, score: 94.309 N N N N
vg0228803563 T -> C LOC_Os02g47180.1 missense_variant ; p.Val84Ala; MODERATE nonsynonymous_codon ; V84A Average:91.787; most accessible tissue: Minghui63 flower, score: 94.309 benign -0.349 TOLERATED 1.00
vg0228803563 T -> C LOC_Os02g47180.2 missense_variant ; p.Val84Ala; MODERATE nonsynonymous_codon ; V84A Average:91.787; most accessible tissue: Minghui63 flower, score: 94.309 benign -0.33 TOLERATED 1.00

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)
vg0228803563 T C -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228803563 NA 3.45E-08 mr1076 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
vg0228803563 NA 2.12E-08 mr1082 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
vg0228803563 NA 3.66E-07 mr1083 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
vg0228803563 NA 6.10E-06 mr1086 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
vg0228803563 NA 1.74E-06 mr1103 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
vg0228803563 NA 3.92E-06 mr1107 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
vg0228803563 NA 2.61E-08 mr1226 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
vg0228803563 NA 4.18E-07 mr1227 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
vg0228803563 NA 6.21E-07 mr1233 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
vg0228803563 NA 1.48E-06 mr1411 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
vg0228803563 NA 6.52E-06 mr1560 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
vg0228803563 4.08E-06 NA mr1072_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
vg0228803563 NA 7.23E-06 mr1072_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
vg0228803563 6.85E-07 NA mr1075_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
vg0228803563 NA 3.55E-06 mr1075_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
vg0228803563 NA 6.27E-06 mr1082_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
vg0228803563 NA 7.86E-06 mr1107_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
vg0228803563 NA 1.32E-06 mr1152_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
vg0228803563 NA 5.58E-06 mr1154_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
vg0228803563 NA 8.57E-07 mr1226_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
vg0228803563 NA 2.34E-07 mr1727_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
vg0228803563 NA 1.55E-07 mr1804_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
vg0228803563 NA 4.49E-06 mr1840_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
vg0228803563 NA 5.60E-07 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