Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0224540597:

Variant ID: vg0224540597 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24540597
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGGTGTGTGGACAGAACAGATTGTCTGATGAACCATGAGTTCCTTTCGACACTTAAGGCTGTTGTTGGCCCGATCTTTCGGTGAGTTGTGATAACTAC[G/A]
ATTTGGGAGAAACGTTGACGATTCGACTACAACCGTACGAGACGTTGTGTTGCGCCTTAGCGATCAATACACCTCTCCGTGGTTTGTTGATCTTGCCGGT

Reverse complement sequence

ACCGGCAAGATCAACAAACCACGGAGAGGTGTATTGATCGCTAAGGCGCAACACAACGTCTCGTACGGTTGTAGTCGAATCGTCAACGTTTCTCCCAAAT[C/T]
GTAGTTATCACAACTCACCGAAAGATCGGGCCAACAACAGCCTTAAGTGTCGAAAGGAACTCATGGTTCATCAGACAATCTGTTCTGTCCACACACCGCC

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 95.50% 0.40% 1.52% 2.54% NA
All Indica  2759 97.70% 0.10% 0.54% 1.67% NA
All Japonica  1512 92.50% 0.90% 2.91% 3.70% NA
Aus  269 92.60% 0.70% 3.35% 3.35% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 95.30% 0.20% 0.99% 3.50% NA
Indica Intermediate  786 97.50% 0.10% 0.76% 1.65% NA
Temperate Japonica  767 97.30% 0.10% 1.04% 1.56% NA
Tropical Japonica  504 88.50% 1.80% 4.56% 5.16% NA
Japonica Intermediate  241 85.90% 1.20% 5.39% 7.47% NA
VI/Aromatic  96 93.80% 2.10% 0.00% 4.17% NA
Intermediate  90 90.00% 0.00% 4.44% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224540597 G -> A LOC_Os02g40470.1 downstream_gene_variant ; 441.0bp to feature; MODIFIER silent_mutation Average:69.343; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0224540597 G -> A LOC_Os02g40480.1 downstream_gene_variant ; 4848.0bp to feature; MODIFIER silent_mutation Average:69.343; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0224540597 G -> A LOC_Os02g40460-LOC_Os02g40470 intergenic_region ; MODIFIER silent_mutation Average:69.343; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0224540597 G -> DEL N N silent_mutation Average:69.343; most accessible tissue: Minghui63 panicle, score: 80.641 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)
vg0224540597 G A 0.01 0.01 0.01 0.01 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224540597 NA 2.66E-07 mr1114 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
vg0224540597 NA 4.13E-06 mr1116 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
vg0224540597 NA 2.41E-07 mr1117 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
vg0224540597 6.21E-06 1.94E-07 mr1119 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
vg0224540597 2.90E-08 9.91E-10 mr1120 Jap_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
vg0224540597 NA 1.57E-06 mr1247 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
vg0224540597 NA 7.53E-07 mr1496 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
vg0224540597 NA 9.65E-06 mr1917 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
vg0224540597 NA 8.54E-08 mr1113_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
vg0224540597 3.88E-07 6.74E-09 mr1114_2 Jap_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
vg0224540597 1.55E-07 1.72E-09 mr1117_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
vg0224540597 2.37E-06 1.86E-08 mr1119_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
vg0224540597 1.13E-06 6.67E-08 mr1120_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
vg0224540597 1.17E-07 8.47E-10 mr1240_2 Jap_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
vg0224540597 2.60E-06 2.34E-07 mr1242_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
vg0224540597 1.71E-06 5.45E-08 mr1247_2 Jap_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
vg0224540597 4.87E-07 4.26E-09 mr1496_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