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Detailed information for vg0911331380:

Variant ID: vg0911331380 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 11331380
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTACCCTCCCCTCCCCTCTCACCAGATGAATCACCGGCCACCTCTCTCCCTTATCTCTGGCCACCTCTCTCCCTTATCTCTTTCCTTCCCTCGTACAGTC[G/A]
GTACGTCAGTCACCATGTGCGTTGCACTGCTATTATTGTTGGTATTTTATTAACTAGTCTCAATCTCTTCTATAGCAGCAGTTGATAAGTCTAAAATTGA

Reverse complement sequence

TCAATTTTAGACTTATCAACTGCTGCTATAGAAGAGATTGAGACTAGTTAATAAAATACCAACAATAATAGCAGTGCAACGCACATGGTGACTGACGTAC[C/T]
GACTGTACGAGGGAAGGAAAGAGATAAGGGAGAGAGGTGGCCAGAGATAAGGGAGAGAGGTGGCCGGTGATTCATCTGGTGAGAGGGGAGGGGAGGGTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.70% 32.20% 0.06% 0.00% NA
All Indica  2759 93.40% 6.60% 0.04% 0.00% NA
All Japonica  1512 16.50% 83.30% 0.13% 0.00% NA
Aus  269 85.90% 14.10% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 89.90% 10.00% 0.11% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 0.00% NA
Temperate Japonica  767 10.00% 89.70% 0.26% 0.00% NA
Tropical Japonica  504 19.40% 80.60% 0.00% 0.00% NA
Japonica Intermediate  241 31.10% 68.90% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg0911331380 G -> A LOC_Os09g18490.1 downstream_gene_variant ; 1205.0bp to feature; MODIFIER silent_mutation Average:66.616; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0911331380 G -> A LOC_Os09g18480-LOC_Os09g18490 intergenic_region ; MODIFIER silent_mutation Average:66.616; most accessible tissue: Zhenshan97 panicle, score: 86.788 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)
vg0911331380 G A -0.02 -0.02 0.0 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0911331380 NA 3.30E-06 mr1051_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
vg0911331380 NA 3.13E-06 mr1072_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
vg0911331380 NA 3.83E-07 mr1075_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
vg0911331380 9.12E-06 2.89E-06 mr1957_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