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Detailed information for vg1121888112:

Variant ID: vg1121888112 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21888112
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGCGACGCGCTTCTCCTCCGGCTTCTGCTGCTGCTGGCGACCCGAGGACTCCCCGGGGACACTACCATTGGCCTGACCCTCCCACTTCCGCTTGGGCGC[C/G]
GGCATTGGCAGCAAGGCCGCGGGCGGCCGCATCGGGGCCCATCTCTCGGCGGTAGGTGGCGGGAGACCGACCGGAGGGCCGAGCTGGCGCGCGGGGAACG

Reverse complement sequence

CGTTCCCCGCGCGCCAGCTCGGCCCTCCGGTCGGTCTCCCGCCACCTACCGCCGAGAGATGGGCCCCGATGCGGCCGCCCGCGGCCTTGCTGCCAATGCC[G/C]
GCGCCCAAGCGGAAGTGGGAGGGTCAGGCCAATGGTAGTGTCCCCGGGGAGTCCTCGGGTCGCCAGCAGCAGCAGAAGCCGGAGGAGAAGCGCGTCGCGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.10% 25.80% 0.06% 0.00% NA
All Indica  2759 97.10% 2.90% 0.00% 0.00% NA
All Japonica  1512 32.80% 67.00% 0.20% 0.00% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 5.20% 0.00% 0.00% NA
Temperate Japonica  767 16.40% 83.30% 0.26% 0.00% NA
Tropical Japonica  504 63.70% 36.30% 0.00% 0.00% NA
Japonica Intermediate  241 20.30% 79.30% 0.41% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg1121888112 C -> G LOC_Os11g37070.1 synonymous_variant ; p.Pro191Pro; LOW synonymous_codon Average:86.751; most accessible tissue: Minghui63 flag leaf, score: 93.673 N N N N
vg1121888112 C -> G LOC_Os11g37070.2 synonymous_variant ; p.Pro191Pro; LOW synonymous_codon Average:86.751; most accessible tissue: Minghui63 flag leaf, score: 93.673 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)
vg1121888112 C G 0.03 0.03 0.03 0.01 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121888112 NA 1.18E-06 mr1629 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
vg1121888112 2.15E-08 2.04E-23 mr1679 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
vg1121888112 NA 6.22E-09 mr1679 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
vg1121888112 NA 2.55E-09 mr1691 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
vg1121888112 NA 2.75E-10 mr1693 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
vg1121888112 NA 1.23E-12 mr1741 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
vg1121888112 NA 1.94E-07 mr1780 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
vg1121888112 2.17E-09 7.38E-28 mr1679_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
vg1121888112 NA 1.47E-07 mr1679_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
vg1121888112 NA 5.99E-08 mr1691_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
vg1121888112 3.90E-06 3.90E-06 mr1760_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