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Detailed information for vg0305607486:

Variant ID: vg0305607486 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 5607486
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCACCGTCTCGCCGCGCTGCTCGGGGAGTGCGACAGGGTGAGGAGCCTCGCCGCCGGGGCGCCCCGGCCGTCGTCCGGCGCCATGGTCGTGCCGTCCA[C/T]
GGTGGTCGGCATGGAGGGCTACCTCGAGGAGGCCCTGGCGTGCCTCGACGACCGCGACGCCGGTGTCGTGGCCATCTGCGGCATGGCCGGCGTCGGCAAG

Reverse complement sequence

CTTGCCGACGCCGGCCATGCCGCAGATGGCCACGACACCGGCGTCGCGGTCGTCGAGGCACGCCAGGGCCTCCTCGAGGTAGCCCTCCATGCCGACCACC[G/A]
TGGACGGCACGACCATGGCGCCGGACGACGGCCGGGGCGCCCCGGCGGCGAGGCTCCTCACCCTGTCGCACTCCCCGAGCAGCGCGGCGAGACGGTGGCG

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 94.10% 5.90% 0.00% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 26.80% 73.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0305607486 C -> T LOC_Os03g10910.1 missense_variant ; p.Thr152Met; MODERATE nonsynonymous_codon ; T152M Average:91.103; most accessible tissue: Minghui63 flag leaf, score: 94.147 unknown unknown DELETERIOUS 0.00

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)
vg0305607486 C T -0.02 -0.02 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0305607486 NA 2.81E-12 mr1231 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
vg0305607486 NA 9.39E-07 mr1762 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
vg0305607486 NA 4.54E-07 mr1762_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