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Detailed information for vg0422855440:

Variant ID: vg0422855440 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22855440
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTGCACGGATGATCGCTAACAATTTCAAACAAAAATTTAAAATTCACTGCAGTTATTACTCCATCCGTTTTAAGTTATAAAATATTCTGAATTTAAT[C/T]
AAAATCAAACTGCTTCAAGTTTGACCAAGTTTATAAATATTTCTATATTTGTCTATAAACTATTTTTTCCGTTTCACAATGTAAGTCATTCTAGCATTTT

Reverse complement sequence

AAAATGCTAGAATGACTTACATTGTGAAACGGAAAAAATAGTTTATAGACAAATATAGAAATATTTATAAACTTGGTCAAACTTGAAGCAGTTTGATTTT[G/A]
ATTAAATTCAGAATATTTTATAACTTAAAACGGATGGAGTAATAACTGCAGTGAATTTTAAATTTTTGTTTGAAATTGTTAGCGATCATCCGTGCAAAAT

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 96.70% 2.10% 1.25% 0.00% NA
All Indica  2759 99.00% 0.10% 0.83% 0.00% NA
All Japonica  1512 91.80% 6.00% 2.18% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.80% 0.00% 2.18% 0.00% NA
Indica II  465 98.90% 0.00% 1.08% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.50% 0.64% 0.00% NA
Temperate Japonica  767 99.20% 0.10% 0.65% 0.00% NA
Tropical Japonica  504 77.40% 17.70% 4.96% 0.00% NA
Japonica Intermediate  241 98.30% 0.40% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 3.33% 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
vg0422855440 C -> T LOC_Os04g38450.1 3_prime_UTR_variant ; 392.0bp to feature; MODIFIER silent_mutation Average:88.206; most accessible tissue: Callus, score: 97.194 N N N N
vg0422855440 C -> T LOC_Os04g38430.2 downstream_gene_variant ; 3796.0bp to feature; MODIFIER silent_mutation Average:88.206; most accessible tissue: Callus, score: 97.194 N N N N
vg0422855440 C -> T LOC_Os04g38430.1 downstream_gene_variant ; 3796.0bp to feature; MODIFIER silent_mutation Average:88.206; most accessible tissue: Callus, score: 97.194 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)
vg0422855440 C T 0.01 0.02 0.02 0.03 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422855440 NA 2.92E-07 mr1076 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
vg0422855440 NA 2.00E-08 mr1082 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
vg0422855440 4.54E-06 5.01E-09 mr1083 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
vg0422855440 1.83E-07 1.11E-09 mr1226 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
vg0422855440 8.97E-10 8.97E-10 mr1076_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
vg0422855440 2.45E-08 2.15E-11 mr1082_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
vg0422855440 1.06E-06 5.40E-10 mr1083_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
vg0422855440 7.92E-06 2.46E-06 mr1103_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
vg0422855440 5.77E-07 6.17E-07 mr1104_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
vg0422855440 7.38E-06 1.58E-06 mr1107_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
vg0422855440 2.04E-06 NA mr1155_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
vg0422855440 6.21E-07 6.68E-09 mr1226_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
vg0422855440 NA 4.50E-06 mr1408_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