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Detailed information for vg0725508857:

Variant ID: vg0725508857 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25508857
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGACCTCGCCTCCTCCGTGGATTGCTGCTGCGTTTGACCGACTGACGCCTTCAAAAAAGGTTCAAAGTGGTGGTGCTTTTTTTTTTTGTGATTCCGG[A/G]
CGGTTGGATGTCGTGTTTCTAGACGGCGATAAGAAGATGTCATATGCGACGGCCTTTTGCTTCTTTTTTTTTTTTTCACTTTGTTGGGAAGTTGGAGCCG

Reverse complement sequence

CGGCTCCAACTTCCCAACAAAGTGAAAAAAAAAAAAAGAAGCAAAAGGCCGTCGCATATGACATCTTCTTATCGCCGTCTAGAAACACGACATCCAACCG[T/C]
CCGGAATCACAAAAAAAAAAAGCACCACCACTTTGAACCTTTTTTGAAGGCGTCAGTCGGTCAAACGCAGCAGCAATCCACGGAGGAGGCGAGGTCACGG

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 37.30% 9.30% 12.17% 41.22% NA
All Indica  2759 5.10% 9.60% 15.66% 69.63% NA
All Japonica  1512 96.80% 2.60% 0.53% 0.13% NA
Aus  269 5.60% 48.70% 44.98% 0.74% NA
Indica I  595 8.20% 6.10% 19.33% 66.39% NA
Indica II  465 6.70% 6.20% 13.33% 73.76% NA
Indica III  913 1.20% 14.10% 15.33% 69.33% NA
Indica Intermediate  786 6.40% 9.00% 14.63% 69.97% NA
Temperate Japonica  767 93.90% 5.10% 0.91% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 95.80% 0.00% 2.08% 2.08% NA
Intermediate  90 56.70% 6.70% 13.33% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0725508857 A -> DEL N N silent_mutation Average:91.948; most accessible tissue: Minghui63 panicle, score: 97.008 N N N N
vg0725508857 A -> G LOC_Os07g42610.1 upstream_gene_variant ; 3558.0bp to feature; MODIFIER silent_mutation Average:91.948; most accessible tissue: Minghui63 panicle, score: 97.008 N N N N
vg0725508857 A -> G LOC_Os07g42620.1 intron_variant ; MODIFIER silent_mutation Average:91.948; most accessible tissue: Minghui63 panicle, score: 97.008 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)
vg0725508857 A G -0.02 -0.03 -0.03 -0.03 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725508857 NA 2.84E-14 mr1062 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
vg0725508857 NA 4.44E-09 mr1336 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
vg0725508857 NA 7.73E-15 mr1386 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
vg0725508857 NA 7.64E-09 mr1514 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
vg0725508857 NA 5.98E-06 mr1035_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
vg0725508857 NA 8.44E-06 mr1252_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
vg0725508857 9.14E-06 9.14E-06 mr1285_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
vg0725508857 NA 2.30E-06 mr1298_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
vg0725508857 NA 2.08E-15 mr1324_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
vg0725508857 6.54E-06 6.54E-06 mr1357_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
vg0725508857 2.59E-06 2.59E-06 mr1382_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
vg0725508857 6.61E-06 9.20E-07 mr1405_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
vg0725508857 NA 7.42E-06 mr1458_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
vg0725508857 4.40E-06 4.40E-06 mr1592_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
vg0725508857 NA 1.25E-31 mr1632_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
vg0725508857 NA 4.13E-06 mr1702_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
vg0725508857 NA 4.60E-06 mr1713_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
vg0725508857 NA 4.00E-06 mr1731_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
vg0725508857 NA 1.80E-06 mr1735_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
vg0725508857 NA 4.17E-08 mr1783_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
vg0725508857 NA 1.88E-07 mr1804_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
vg0725508857 NA 1.12E-06 mr1914_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