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Detailed information for vg0401150253:

Variant ID: vg0401150253 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1150253
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTACTCACAGGACAAGCATCTCAGCCATTGTGTGGAATGGCCTGAGAATATAGTATTACCTAGACTGCAAGGTTGAAAACACATGATAAGTTTGGTTATC[C/T]
GGACCTAAATAGTTGGTGGTTCAGAGAATTCATGCCTACTGCGTGCTGTAAACAAACAAAAACGGAGTTTTTTTTTCCCTTGTGCAATAGGATGATAATG

Reverse complement sequence

CATTATCATCCTATTGCACAAGGGAAAAAAAAACTCCGTTTTTGTTTGTTTACAGCACGCAGTAGGCATGAATTCTCTGAACCACCAACTATTTAGGTCC[G/A]
GATAACCAAACTTATCATGTGTTTTCAACCTTGCAGTCTAGGTAATACTATATTCTCAGGCCATTCCACACAATGGCTGAGATGCTTGTCCTGTGAGTAA

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 85.60% 14.30% 0.06% 0.00% NA
All Indica  2759 85.80% 14.20% 0.00% 0.00% NA
All Japonica  1512 92.60% 7.30% 0.07% 0.00% NA
Aus  269 66.90% 33.10% 0.00% 0.00% NA
Indica I  595 84.50% 15.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 79.70% 20.30% 0.00% 0.00% NA
Indica Intermediate  786 87.30% 12.70% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 87.90% 12.10% 0.00% 0.00% NA
Japonica Intermediate  241 80.10% 19.50% 0.41% 0.00% NA
VI/Aromatic  96 20.80% 77.10% 2.08% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 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
vg0401150253 C -> T LOC_Os04g02910.1 intron_variant ; MODIFIER silent_mutation Average:86.068; most accessible tissue: Minghui63 young leaf, score: 94.396 N N N N
vg0401150253 C -> T LOC_Os04g02910.3 intron_variant ; MODIFIER silent_mutation Average:86.068; most accessible tissue: Minghui63 young leaf, score: 94.396 N N N N
vg0401150253 C -> T LOC_Os04g02910.4 intron_variant ; MODIFIER silent_mutation Average:86.068; most accessible tissue: Minghui63 young leaf, score: 94.396 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)
vg0401150253 C T 0.03 0.02 0.0 -0.01 0.02 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401150253 NA 1.93E-06 mr1086 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
vg0401150253 NA 4.15E-06 mr1088 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
vg0401150253 NA 1.92E-06 mr1210 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
vg0401150253 NA 3.32E-08 mr1213 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
vg0401150253 6.78E-06 1.97E-06 mr1337 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
vg0401150253 8.30E-06 8.30E-06 mr1381 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
vg0401150253 7.70E-07 NA mr1878 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
vg0401150253 NA 7.53E-07 mr1878 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
vg0401150253 NA 3.00E-06 mr1265_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