Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0203949121:

Variant ID: vg0203949121 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3949121
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AAACCTTCAGAGGCTTGTGCGGCCACCCCACCAACTGCATCGCCTGCTGCACCAACGAGGGCTACACAGGAGGCTACTGCACAACTGTTAGACACAAATG[C/A]
ATGTGCACCAAAGCGTGTGGAGGGGAGAGTCCGCCTGATGATCCGCCGTCGGCGATGCCGGCATCGCCAGTGACGACGACAAGAGCCTGATCGCTGAAAA

Reverse complement sequence

TTTTCAGCGATCAGGCTCTTGTCGTCGTCACTGGCGATGCCGGCATCGCCGACGGCGGATCATCAGGCGGACTCTCCCCTCCACACGCTTTGGTGCACAT[G/T]
CATTTGTGTCTAACAGTTGTGCAGTAGCCTCCTGTGTAGCCCTCGTTGGTGCAGCAGGCGATGCAGTTGGTGGGGTGGCCGCACAAGCCTCTGAAGGTTT

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 72.90% 24.50% 2.37% 0.15% NA
All Indica  2759 54.50% 41.40% 3.88% 0.25% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 47.40% 43.90% 8.74% 0.00% NA
Indica II  465 31.00% 67.30% 1.72% 0.00% NA
Indica III  913 73.60% 25.60% 0.66% 0.11% NA
Indica Intermediate  786 51.50% 42.50% 5.22% 0.76% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 17.80% 4.44% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0203949121 C -> A LOC_Os02g07628.1 stop_gained ; p.Cys64*; HIGH stop_gained Average:81.98; most accessible tissue: Zhenshan97 panicle, score: 88.625 N N N N
vg0203949121 C -> DEL LOC_Os02g07628.1 N frameshift_variant Average:81.98; most accessible tissue: Zhenshan97 panicle, score: 88.625 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)
vg0203949121 C A -0.04 -0.01 -0.01 -0.02 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203949121 NA 6.95E-11 mr1352 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
vg0203949121 NA 1.81E-06 mr1352 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
vg0203949121 NA 5.84E-08 mr1739 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
vg0203949121 NA 1.26E-06 mr1588_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
vg0203949121 NA 1.47E-10 mr1739_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