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Detailed information for vg0609896396:

Variant ID: vg0609896396 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9896396
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGAAATTCAAATTTTATGTAGGTCAATTAAACTCAGATGGAGAAATAACCAAAATAAAATTGGTAGATCTCAATAAGTTATACAACTTTGTTTTTGA[C/T]
AATATTTTCACATAAGTTCATTTAGTAAGATAAAATTCGACTCGAAGGTTTAATATTTTGAAATTAATTGAAAGGAGGGAGGCAAAATGGACTTCTCGGC

Reverse complement sequence

GCCGAGAAGTCCATTTTGCCTCCCTCCTTTCAATTAATTTCAAAATATTAAACCTTCGAGTCGAATTTTATCTTACTAAATGAACTTATGTGAAAATATT[G/A]
TCAAAAACAAAGTTGTATAACTTATTGAGATCTACCAATTTTATTTTGGTTATTTCTCCATCTGAGTTTAATTGACCTACATAAAATTTGAATTTCAAAT

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 92.30% 7.70% 0.02% 0.00% NA
All Indica  2759 87.90% 12.10% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 85.60% 14.40% 0.00% 0.00% NA
Indica III  913 82.50% 17.50% 0.00% 0.00% NA
Indica Intermediate  786 86.30% 13.60% 0.13% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0609896396 C -> T LOC_Os06g17060.1 upstream_gene_variant ; 4399.0bp to feature; MODIFIER silent_mutation Average:78.523; most accessible tissue: Minghui63 young leaf, score: 88.753 N N N N
vg0609896396 C -> T LOC_Os06g17070.1 upstream_gene_variant ; 1228.0bp to feature; MODIFIER silent_mutation Average:78.523; most accessible tissue: Minghui63 young leaf, score: 88.753 N N N N
vg0609896396 C -> T LOC_Os06g17070-LOC_Os06g17080 intergenic_region ; MODIFIER silent_mutation Average:78.523; most accessible tissue: Minghui63 young leaf, score: 88.753 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)
vg0609896396 C T -0.09 -0.07 -0.06 -0.06 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609896396 NA 2.49E-09 mr1090 Ind_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
vg0609896396 9.04E-06 NA mr1121 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
vg0609896396 NA 2.60E-07 mr1121 Ind_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
vg0609896396 1.25E-06 NA mr1211 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
vg0609896396 2.52E-06 5.84E-11 mr1211 Ind_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
vg0609896396 3.70E-06 NA mr1068_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
vg0609896396 3.51E-06 NA mr1090_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
vg0609896396 3.58E-06 4.30E-10 mr1090_2 Ind_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
vg0609896396 9.75E-07 NA mr1121_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
vg0609896396 5.75E-06 9.61E-08 mr1121_2 Ind_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
vg0609896396 2.71E-07 NA mr1211_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
vg0609896396 5.40E-07 9.18E-12 mr1211_2 Ind_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