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Detailed information for vg0422772120:

Variant ID: vg0422772120 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22772120
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGCCGCCTGGTCCGACGACTCGCCGCCGCTGCCGTGGTGCTTGATCCGACAACTCCACGACCAATTCGCTGCCTCGGCTGCCAACACCCCCGCCGTTGC[C/T]
GTGGCACCTGGTCCGACCTCTCCACGGCCACCTCGCCATCGCGGCCGGCAACGCCCCAACCGCCACCGCAGCCGCCTGCCATGGCCGTCGACGCCAAGAC

Reverse complement sequence

GTCTTGGCGTCGACGGCCATGGCAGGCGGCTGCGGTGGCGGTTGGGGCGTTGCCGGCCGCGATGGCGAGGTGGCCGTGGAGAGGTCGGACCAGGTGCCAC[G/A]
GCAACGGCGGGGGTGTTGGCAGCCGAGGCAGCGAATTGGTCGTGGAGTTGTCGGATCAAGCACCACGGCAGCGGCGGCGAGTCGTCGGACCAGGCGGCGG

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 78.10% 5.00% 5.23% 11.74% NA
All Indica  2759 79.20% 0.50% 2.10% 18.19% NA
All Japonica  1512 73.50% 13.70% 11.44% 1.39% NA
Aus  269 88.80% 0.00% 1.12% 10.04% NA
Indica I  595 80.50% 0.00% 2.52% 16.97% NA
Indica II  465 80.20% 1.50% 1.94% 16.34% NA
Indica III  913 78.90% 0.20% 1.75% 19.17% NA
Indica Intermediate  786 77.90% 0.80% 2.29% 19.08% NA
Temperate Japonica  767 92.00% 3.10% 4.82% 0.00% NA
Tropical Japonica  504 38.50% 32.70% 24.60% 4.17% NA
Japonica Intermediate  241 87.60% 7.50% 4.98% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 3.12% 0.00% NA
Intermediate  90 71.10% 12.20% 11.11% 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
vg0422772120 C -> DEL N N silent_mutation Average:51.467; most accessible tissue: Zhenshan97 flag leaf, score: 92.201 N N N N
vg0422772120 C -> T LOC_Os04g38270.1 downstream_gene_variant ; 1348.0bp to feature; MODIFIER silent_mutation Average:51.467; most accessible tissue: Zhenshan97 flag leaf, score: 92.201 N N N N
vg0422772120 C -> T LOC_Os04g38260-LOC_Os04g38270 intergenic_region ; MODIFIER silent_mutation Average:51.467; most accessible tissue: Zhenshan97 flag leaf, score: 92.201 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)
vg0422772120 C T -0.04 -0.02 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422772120 3.95E-06 NA mr1070_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
vg0422772120 1.93E-06 5.99E-06 mr1085_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
vg0422772120 5.83E-06 5.83E-06 mr1145_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
vg0422772120 NA 5.26E-06 mr1155_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
vg0422772120 8.76E-06 NA mr1227_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
vg0422772120 8.41E-06 1.41E-06 mr1246_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
vg0422772120 2.43E-06 3.63E-07 mr1250_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
vg0422772120 1.58E-06 1.04E-06 mr1404_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
vg0422772120 3.19E-06 NA mr1408_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
vg0422772120 1.51E-06 7.32E-07 mr1620_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
vg0422772120 5.37E-07 4.16E-06 mr1949_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