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Detailed information for vg0223990288:

Variant ID: vg0223990288 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23990288
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.06, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CGACGCCGACATCCACTCGGCGAACCCGCTCGCGCGCAGGCACGAGCGCCTCCCCGTCGCGCCCTTCTTCGGCCCGCTCGCCGACGCGCCGCAGCCCTTC[C/A]
CCTTCTCCCAGGCCGCCGCGGATGCCGCCGCGGCGCGGGAGGAGGATGCGGATGATGACCGGAGCAACGAGGCCGAGGCGGCGTCGTGGCTTCTCCCCGA

Reverse complement sequence

TCGGGGAGAAGCCACGACGCCGCCTCGGCCTCGTTGCTCCGGTCATCATCCGCATCCTCCTCCCGCGCCGCGGCGGCATCCGCGGCGGCCTGGGAGAAGG[G/T]
GAAGGGCTGCGGCGCGTCGGCGAGCGGGCCGAAGAAGGGCGCGACGGGGAGGCGCTCGTGCCTGCGCGCGAGCGGGTTCGCCGAGTGGATGTCGGCGTCG

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 55.80% 44.00% 0.21% 0.00% NA
All Indica  2759 35.70% 64.00% 0.29% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 33.50% 65.80% 0.74% 0.00% NA
Indica I  595 18.80% 80.50% 0.67% 0.00% NA
Indica II  465 22.80% 77.20% 0.00% 0.00% NA
Indica III  913 52.20% 47.60% 0.11% 0.00% NA
Indica Intermediate  786 37.00% 62.60% 0.38% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 7.70% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 0.00% 0.00% NA

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

CategoryVariant IDChromPosGeneMSURAPAlt_Allele_FunctionRef_genoAlt_geno
Heading datevg0223990288Chr223990288OsCOL4LOC_Os02g39710Os02g0610500promoting heading dateCA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0223990288 C -> A LOC_Os02g39710.1 missense_variant ; p.Pro129Thr; MODERATE nonsynonymous_codon ; P129T Average:94.745; most accessible tissue: Minghui63 flag leaf, score: 99.018 unknown unknown TOLERATED 0.64

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)
vg0223990288 C A -0.02 -0.02 -0.02 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223990288 NA 5.69E-06 mr1100 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
vg0223990288 NA 6.01E-09 mr1222_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