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Detailed information for vg0605964534:

Variant ID: vg0605964534 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5964534
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATAATGTGTGTATGACAGGTAAGACCAGATATTACTAGTATAGTAAGTAACTAGTGTATGAATTAGATATTACATTGGCTATAAATGATTTGAAGCTAG[T/C]
AGTGGGCTTTGCTATTAAACTTGCTCGGGGAAAAGAAGAGCTGCACGCCGGGGGGATTCCCTGTTCCGACGCGGGCCGTGTGGCTGTGGATGTGGCTCTA

Reverse complement sequence

TAGAGCCACATCCACAGCCACACGGCCCGCGTCGGAACAGGGAATCCCCCCGGCGTGCAGCTCTTCTTTTCCCCGAGCAAGTTTAATAGCAAAGCCCACT[A/G]
CTAGCTTCAAATCATTTATAGCCAATGTAATATCTAATTCATACACTAGTTACTTACTATACTAGTAATATCTGGTCTTACCTGTCATACACACATTATG

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 79.30% 20.30% 0.38% 0.00% NA
All Indica  2759 92.40% 7.50% 0.14% 0.00% NA
All Japonica  1512 50.30% 48.80% 0.86% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 84.70% 15.10% 0.17% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.30% 3.60% 0.11% 0.00% NA
Indica Intermediate  786 90.70% 9.00% 0.25% 0.00% NA
Temperate Japonica  767 35.30% 63.20% 1.43% 0.00% NA
Tropical Japonica  504 73.40% 26.40% 0.20% 0.00% NA
Japonica Intermediate  241 49.80% 49.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0605964534 T -> C LOC_Os06g11330.1 upstream_gene_variant ; 1350.0bp to feature; MODIFIER silent_mutation Average:89.735; most accessible tissue: Zhenshan97 flag leaf, score: 95.744 N N N N
vg0605964534 T -> C LOC_Os06g11340.1 downstream_gene_variant ; 984.0bp to feature; MODIFIER silent_mutation Average:89.735; most accessible tissue: Zhenshan97 flag leaf, score: 95.744 N N N N
vg0605964534 T -> C LOC_Os06g11350.1 downstream_gene_variant ; 984.0bp to feature; MODIFIER silent_mutation Average:89.735; most accessible tissue: Zhenshan97 flag leaf, score: 95.744 N N N N
vg0605964534 T -> C LOC_Os06g11330-LOC_Os06g11340 intergenic_region ; MODIFIER silent_mutation Average:89.735; most accessible tissue: Zhenshan97 flag leaf, score: 95.744 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)
vg0605964534 T C 0.06 0.01 -0.02 0.07 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605964534 1.79E-06 NA mr1679 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