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Detailed information for vg1202908436:

Variant ID: vg1202908436 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2908436
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTACTGCTAGCTACTACTCCAGCTGGTATAGTACTGATCTTACCTGTGTTGTTGCTACTGTGTGTGTACTGCAACTGCAGGTGCGGTCGATGACGATG[G/A]
CACTATCCGAAACTCTTTTTTTTTTTAGTATAGAGGGCCCCTCCCATTTCCAGTTAAGAAATGAGCAACAATTTCCACGAGTTATTTAAAAGGATACGTA

Reverse complement sequence

TACGTATCCTTTTAAATAACTCGTGGAAATTGTTGCTCATTTCTTAACTGGAAATGGGAGGGGCCCTCTATACTAAAAAAAAAAAGAGTTTCGGATAGTG[C/T]
CATCGTCATCGACCGCACCTGCAGTTGCAGTACACACACAGTAGCAACAACACAGGTAAGATCAGTACTATACCAGCTGGAGTAGTAGCTAGCAGTAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 5.80% 0.08% 0.00% NA
All Indica  2759 96.10% 3.80% 0.11% 0.00% NA
All Japonica  1512 97.40% 2.60% 0.00% 0.00% NA
Aus  269 52.40% 47.20% 0.37% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 93.60% 6.10% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1202908436 G -> A LOC_Os12g06160.1 downstream_gene_variant ; 2837.0bp to feature; MODIFIER silent_mutation Average:68.394; most accessible tissue: Callus, score: 95.514 N N N N
vg1202908436 G -> A LOC_Os12g06150-LOC_Os12g06160 intergenic_region ; MODIFIER silent_mutation Average:68.394; most accessible tissue: Callus, score: 95.514 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)
vg1202908436 G A 0.25 0.06 0.02 -0.06 0.03 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202908436 8.37E-06 NA mr1549 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
vg1202908436 9.62E-08 NA mr1757 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
vg1202908436 8.08E-06 NA mr1539_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