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Detailed information for vg0328116174:

Variant ID: vg0328116174 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28116174
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGACCAGGCGTAGTATCGCGTATATGCCCTCGTCTCGACTCCGCCGTAATCTGATTCGGCCGCGGTCTTCTTCTGGAGAATATTATGCTTGCTCATTTTA[T/A]
GCTGTGTTTAGTTGGTGAAAAGAAAATTTTTAAGTGTCACATTAAACTTTTGATTGGATGTTAAAATGAGTTCTCAGACACGATTAAAAAACTAATTTCA

Reverse complement sequence

TGAAATTAGTTTTTTAATCGTGTCTGAGAACTCATTTTAACATCCAATCAAAAGTTTAATGTGACACTTAAAAATTTTCTTTTCACCAACTAAACACAGC[A/T]
TAAAATGAGCAAGCATAATATTCTCCAGAAGAAGACCGCGGCCGAATCAGATTACGGCGGAGTCGAGACGAGGGCATATACGCGATACTACGCCTGGTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 11.10% 0.02% 0.00% NA
All Indica  2759 92.00% 8.00% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 2.20% 97.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 85.10% 14.90% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 6.40% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0328116174 T -> A LOC_Os03g49400.1 upstream_gene_variant ; 446.0bp to feature; MODIFIER silent_mutation Average:86.509; most accessible tissue: Minghui63 panicle, score: 96.34 N N N N
vg0328116174 T -> A LOC_Os03g49380.1 downstream_gene_variant ; 2874.0bp to feature; MODIFIER silent_mutation Average:86.509; most accessible tissue: Minghui63 panicle, score: 96.34 N N N N
vg0328116174 T -> A LOC_Os03g49380.2 downstream_gene_variant ; 2888.0bp to feature; MODIFIER silent_mutation Average:86.509; most accessible tissue: Minghui63 panicle, score: 96.34 N N N N
vg0328116174 T -> A LOC_Os03g49380.3 downstream_gene_variant ; 2874.0bp to feature; MODIFIER silent_mutation Average:86.509; most accessible tissue: Minghui63 panicle, score: 96.34 N N N N
vg0328116174 T -> A LOC_Os03g49380-LOC_Os03g49400 intergenic_region ; MODIFIER silent_mutation Average:86.509; most accessible tissue: Minghui63 panicle, score: 96.34 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)
vg0328116174 T A -0.01 0.0 0.02 0.03 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328116174 NA 4.46E-06 mr1073 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
vg0328116174 NA 2.84E-27 mr1168 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
vg0328116174 NA 3.41E-06 mr1230 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
vg0328116174 NA 3.79E-08 mr1320 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
vg0328116174 NA 9.15E-07 mr1382 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
vg0328116174 NA 1.71E-25 mr1383 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
vg0328116174 NA 9.71E-07 mr1420 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
vg0328116174 NA 5.90E-07 mr1453 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
vg0328116174 NA 1.69E-06 mr1545 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
vg0328116174 NA 1.72E-06 mr1556 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
vg0328116174 NA 5.16E-11 mr1696 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
vg0328116174 NA 4.25E-10 mr1730 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
vg0328116174 NA 3.34E-23 mr1817 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
vg0328116174 NA 2.79E-11 mr1846 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
vg0328116174 NA 2.14E-14 mr1909 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
vg0328116174 NA 1.21E-12 mr1921 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
vg0328116174 NA 9.86E-06 mr1158_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
vg0328116174 NA 1.55E-21 mr1817_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
vg0328116174 NA 1.42E-17 mr1846_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