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Detailed information for vg0701510236:

Variant ID: vg0701510236 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 1510236
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAGCGGGTAATAGTAGAGAATGTCCTCATCATACAATATGAGAAAAATGGATTATTACTTAATTAATTAACAAACGCTAGAAATCACAACGTACTCGA[T/C]
AGAATAAAAAAAAATATGTGTTAGGACATGAGGCATATCATACCATCGAGTACGTGTATATACTTTTGTGCATGCATCCGTTAACCTATGCGTGTATGTG

Reverse complement sequence

CACATACACGCATAGGTTAACGGATGCATGCACAAAAGTATATACACGTACTCGATGGTATGATATGCCTCATGTCCTAACACATATTTTTTTTTATTCT[A/G]
TCGAGTACGTTGTGATTTCTAGCGTTTGTTAATTAATTAAGTAATAATCCATTTTTCTCATATTGTATGATGAGGACATTCTCTACTATTACCCGCTGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.10% 13.90% 0.02% 0.00% NA
All Indica  2759 82.30% 17.70% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 40.10% 59.90% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 70.30% 29.70% 0.00% 0.00% NA
Indica III  913 82.40% 17.60% 0.00% 0.00% NA
Indica Intermediate  786 76.30% 23.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0701510236 T -> C LOC_Os07g03710.1 upstream_gene_variant ; 1789.0bp to feature; MODIFIER silent_mutation Average:71.382; most accessible tissue: Minghui63 root, score: 92.181 N N N N
vg0701510236 T -> C LOC_Os07g03700-LOC_Os07g03710 intergenic_region ; MODIFIER silent_mutation Average:71.382; most accessible tissue: Minghui63 root, score: 92.181 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)
vg0701510236 T C 0.04 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0701510236 1.85E-06 NA Heading_date Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0701510236 NA 2.03E-06 mr1174 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
vg0701510236 NA 1.14E-06 mr1188 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
vg0701510236 NA 4.35E-07 mr1188_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
vg0701510236 NA 6.27E-10 mr1510_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
vg0701510236 NA 3.20E-07 mr1691_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
vg0701510236 NA 4.24E-07 mr1702_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