Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1105592709:

Variant ID: vg1105592709 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5592709
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAAATATCCAATTCAGAGCACTCTCAGGATATGCCACTCAATTCGTAGCACTTTTATATTATGCCACTAGGAGTGTGAATTCCTTTTTTCCCATGCCAC[T/A]
TTTTGTCGTTCAATGTCAACTCTCCACCCTCGACACGCCGGCGAGTTTCTCCGTCCACCACATGCCAACGCCTGTGGGATGGACAACGAGTTCGTCCGTC

Reverse complement sequence

GACGGACGAACTCGTTGTCCATCCCACAGGCGTTGGCATGTGGTGGACGGAGAAACTCGCCGGCGTGTCGAGGGTGGAGAGTTGACATTGAACGACAAAA[A/T]
GTGGCATGGGAAAAAAGGAATTCACACTCCTAGTGGCATAATATAAAAGTGCTACGAATTGAGTGGCATATCCTGAGAGTGCTCTGAATTGGATATTTGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.70% 39.30% 0.06% 0.00% NA
All Indica  2759 88.70% 11.20% 0.07% 0.00% NA
All Japonica  1512 6.80% 93.10% 0.07% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 84.00% 16.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 88.10% 11.80% 0.11% 0.00% NA
Indica Intermediate  786 87.80% 12.10% 0.13% 0.00% NA
Temperate Japonica  767 2.60% 97.40% 0.00% 0.00% NA
Tropical Japonica  504 13.10% 86.90% 0.00% 0.00% NA
Japonica Intermediate  241 7.10% 92.50% 0.41% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1105592709 T -> A LOC_Os11g10310.1 3_prime_UTR_variant ; 515.0bp to feature; MODIFIER silent_mutation Average:81.924; most accessible tissue: Minghui63 flag leaf, score: 91.823 N N N N
vg1105592709 T -> A LOC_Os11g10290.1 upstream_gene_variant ; 3509.0bp to feature; MODIFIER silent_mutation Average:81.924; most accessible tissue: Minghui63 flag leaf, score: 91.823 N N N N
vg1105592709 T -> A LOC_Os11g10300.1 upstream_gene_variant ; 256.0bp to feature; MODIFIER silent_mutation Average:81.924; most accessible tissue: Minghui63 flag leaf, score: 91.823 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)
vg1105592709 T A -0.06 -0.04 -0.04 -0.04 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105592709 NA 1.18E-08 mr1302 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
vg1105592709 NA 4.75E-07 mr1315 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
vg1105592709 NA 1.49E-06 mr1392 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
vg1105592709 NA 4.29E-08 mr1488 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
vg1105592709 NA 4.69E-13 mr1521 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
vg1105592709 NA 7.59E-14 mr1653 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
vg1105592709 NA 1.23E-10 mr1683 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
vg1105592709 NA 8.34E-08 mr1779 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
vg1105592709 NA 1.93E-07 mr1810 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
vg1105592709 7.50E-07 2.68E-06 mr1931 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
vg1105592709 NA 7.82E-07 mr1979 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