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Detailed information for vg1127311930:

Variant ID: vg1127311930 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27311930
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGAACTCTGGTTGTCTTTCCTTATCCAAAACTCCCTCCATATCTGAAGTCAGTTTCCGTATAAGACATGGTATGTGGTGGGTCCTGCCGAGATATAGT[C/T]
GACTACTATTAGGTATGTGGTATCCATAACCCTGACAGTCGCCCATGTAACCCTAGCCGCGCGTGCGTGTGTGCTGTGGGGAAGCGGCACGCGGGCGTGT

Reverse complement sequence

ACACGCCCGCGTGCCGCTTCCCCACAGCACACACGCACGCGCGGCTAGGGTTACATGGGCGACTGTCAGGGTTATGGATACCACATACCTAATAGTAGTC[G/A]
ACTATATCTCGGCAGGACCCACCACATACCATGTCTTATACGGAAACTGACTTCAGATATGGAGGGAGTTTTGGATAAGGAAAGACAACCAGAGTTCTAC

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 71.20% 1.40% 1.21% 26.11% NA
All Indica  2759 70.30% 0.40% 1.12% 28.16% NA
All Japonica  1512 73.80% 2.40% 1.26% 22.49% NA
Aus  269 58.70% 5.60% 1.86% 33.83% NA
Indica I  595 95.30% 0.00% 0.34% 4.37% NA
Indica II  465 59.80% 0.00% 1.72% 38.49% NA
Indica III  913 61.10% 1.20% 1.75% 35.93% NA
Indica Intermediate  786 68.30% 0.00% 0.64% 31.04% NA
Temperate Japonica  767 88.30% 2.10% 0.65% 9.00% NA
Tropical Japonica  504 60.10% 3.40% 1.39% 35.12% NA
Japonica Intermediate  241 56.40% 1.70% 2.90% 39.00% NA
VI/Aromatic  96 82.30% 3.10% 0.00% 14.58% NA
Intermediate  90 82.20% 2.20% 2.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127311930 C -> T LOC_Os11g45120.1 downstream_gene_variant ; 2103.0bp to feature; MODIFIER silent_mutation Average:77.659; most accessible tissue: Minghui63 flag leaf, score: 96.674 N N N N
vg1127311930 C -> T LOC_Os11g45120-LOC_Os11g45130 intergenic_region ; MODIFIER silent_mutation Average:77.659; most accessible tissue: Minghui63 flag leaf, score: 96.674 N N N N
vg1127311930 C -> DEL N N silent_mutation Average:77.659; most accessible tissue: Minghui63 flag leaf, score: 96.674 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)
vg1127311930 C T 0.02 -0.01 0.0 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127311930 NA 6.79E-07 mr1038_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
vg1127311930 3.28E-06 3.28E-06 mr1141_2 Jap_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
vg1127311930 4.13E-09 4.13E-09 mr1191_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