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Detailed information for vg1200350921:

Variant ID: vg1200350921 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 350921
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGTCTGTCGCCGCCGCCGCGCTTGTCCTAACCCCCACTCCAACGCTCAACCGTCTCTCCTTTCCCTTCGCCCACCGTCACTGCCCTAGTACTGCTGCT[C/A]
CTCGGTGGAGGCCCGCGCGGTGCCGCGGGAAGCCGGCGGTGGAGGACGTGGTACACGACGACGAGGAGGAGACCTGGCGGCGGGAGGCCAACCCCGAGAG

Reverse complement sequence

CTCTCGGGGTTGGCCTCCCGCCGCCAGGTCTCCTCCTCGTCGTCGTGTACCACGTCCTCCACCGCCGGCTTCCCGCGGCACCGCGCGGGCCTCCACCGAG[G/T]
AGCAGCAGTACTAGGGCAGTGACGGTGGGCGAAGGGAAAGGAGAGACGGTTGAGCGTTGGAGTGGGGGTTAGGACAAGCGCGGCGGCGGCGACAGACCTC

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 79.90% 20.00% 0.15% 0.00% NA
All Indica  2759 68.00% 31.80% 0.22% 0.00% NA
All Japonica  1512 96.90% 3.00% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 26.50% 72.70% 0.86% 0.00% NA
Indica III  913 72.70% 27.20% 0.11% 0.00% NA
Indica Intermediate  786 66.50% 33.30% 0.13% 0.00% NA
Temperate Japonica  767 95.60% 4.40% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg1200350921 C -> A LOC_Os12g01580.1 missense_variant ; p.Pro42Thr; MODERATE nonsynonymous_codon ; P42T Average:97.014; most accessible tissue: Minghui63 flag leaf, score: 98.97 unknown unknown TOLERATED 0.41

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)
vg1200350921 C A 0.0 0.0 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
vg1200350921 NA 9.36E-17 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1200350921 NA 8.33E-18 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1200350921 NA 2.10E-09 mr1174 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
vg1200350921 NA 4.02E-09 mr1174_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