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Detailed information for vg1207719912:

Variant ID: vg1207719912 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7719912
Reference Allele: CAlternative Allele: G,T
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTCAAGGGCTGCGGGCGAAGAGGTTTCGCCACACCCACGCCCTTCGCCATAGTGCCAATAAGGCACGGCGTCAAGGGCTGCGGGCGAAGAGGTTTCGC[C/G,T]
AACCCTTGCCCTTCGCCATAGTGCCAATAAGGCACGGCGTCAAGGGCTACGGGCGAAGAGGTTTCGCCACACGCCTTGCCCTTCGCCATAGTGCCAATAA

Reverse complement sequence

TTATTGGCACTATGGCGAAGGGCAAGGCGTGTGGCGAAACCTCTTCGCCCGTAGCCCTTGACGCCGTGCCTTATTGGCACTATGGCGAAGGGCAAGGGTT[G/C,A]
GCGAAACCTCTTCGCCCGCAGCCCTTGACGCCGTGCCTTATTGGCACTATGGCGAAGGGCGTGGGTGTGGCGAAACCTCTTCGCCCGCAGCCCTTGACGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 0.90% 2.26% 0.00% T: 0.02%
All Indica  2759 99.50% 0.10% 0.36% 0.00% T: 0.04%
All Japonica  1512 91.10% 2.70% 6.15% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.00% 0.00% 1.01% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.10% 0.11% 0.00% T: 0.11%
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 92.40% 1.80% 5.74% 0.00% NA
Tropical Japonica  504 92.10% 2.80% 5.16% 0.00% NA
Japonica Intermediate  241 85.10% 5.40% 9.54% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg1207719912 C -> G LOC_Os12g13690.1 missense_variant ; p.Leu53Phe; MODERATE nonsynonymous_codon ; L53F Average:74.173; most accessible tissue: Minghui63 flag leaf, score: 93.546 unknown unknown TOLERATED 0.57
vg1207719912 C -> T LOC_Os12g13690.1 synonymous_variant ; p.Leu53Leu; LOW synonymous_codon Average:74.173; most accessible tissue: Minghui63 flag leaf, score: 93.546 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)
vg1207719912 C G -0.02 -0.01 -0.01 -0.01 -0.01 -0.05
vg1207719912 C T -0.01 -0.01 -0.01 -0.01 -0.01 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207719912 2.06E-06 2.05E-06 mr1197_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
vg1207719912 NA 6.61E-06 mr1556_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
vg1207719912 5.48E-06 5.48E-06 mr1756_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
vg1207719912 NA 8.16E-06 mr1974_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