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Detailed information for vg0309326904:

Variant ID: vg0309326904 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 9326904
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCCTATAAAACCACCAAGGAGCTAAATTGCACCGGTTTTAAGAGTTGTGGGTCGAGATATCCAGTTATGTGGTTTAGGGTTACGAATTAGATTTCGATC[C/T,A]
CTTTTAAGGGTCACAAAGTGAACTTATTCCACAGCTCGGTTCGGTGGCTTGAGCAGCTTTGCAGGCTTGCAGCACGTCGGCCCATCCCAAGTCCCAACCC

Reverse complement sequence

GGGTTGGGACTTGGGATGGGCCGACGTGCTGCAAGCCTGCAAAGCTGCTCAAGCCACCGAACCGAGCTGTGGAATAAGTTCACTTTGTGACCCTTAAAAG[G/A,T]
GATCGAAATCTAATTCGTAACCCTAAACCACATAACTGGATATCTCGACCCACAACTCTTAAAACCGGTGCAATTTAGCTCCTTGGTGGTTTTATAGGGT

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 94.80% 4.70% 0.42% 0.00% A: 0.06%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 84.30% 14.40% 1.26% 0.00% A: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 55.00% 41.30% 3.57% 0.00% A: 0.20%
Japonica Intermediate  241 96.70% 2.90% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 1.11% 0.00% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0309326904 C -> T LOC_Os03g16824.1 upstream_gene_variant ; 2503.0bp to feature; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 N N N N
vg0309326904 C -> T LOC_Os03g16812.1 downstream_gene_variant ; 887.0bp to feature; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 N N N N
vg0309326904 C -> T LOC_Os03g16812-LOC_Os03g16824 intergenic_region ; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 N N N N
vg0309326904 C -> A LOC_Os03g16824.1 upstream_gene_variant ; 2503.0bp to feature; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 N N N N
vg0309326904 C -> A LOC_Os03g16812.1 downstream_gene_variant ; 887.0bp to feature; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 N N N N
vg0309326904 C -> A LOC_Os03g16812-LOC_Os03g16824 intergenic_region ; MODIFIER silent_mutation Average:98.546; most accessible tissue: Minghui63 root, score: 99.46 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)
vg0309326904 C A 0.01 0.01 0.01 0.0 0.01 0.01
vg0309326904 C T 0.02 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0309326904 NA 2.57E-08 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
vg0309326904 NA 7.60E-09 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
vg0309326904 2.40E-06 1.78E-10 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
vg0309326904 5.17E-06 5.17E-06 mr1085 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
vg0309326904 NA 8.10E-09 mr1226 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
vg0309326904 NA 1.60E-06 mr1408 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
vg0309326904 NA 5.10E-06 mr1411 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
vg0309326904 NA 7.38E-06 mr1560 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
vg0309326904 NA 1.48E-06 mr1949 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
vg0309326904 3.29E-06 3.29E-06 mr1076_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
vg0309326904 1.86E-06 8.50E-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
vg0309326904 3.01E-07 1.00E-11 mr1083_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
vg0309326904 NA 8.31E-07 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
vg0309326904 2.86E-06 1.03E-08 mr1104_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
vg0309326904 1.75E-06 1.13E-08 mr1107_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
vg0309326904 4.16E-07 4.16E-07 mr1145_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
vg0309326904 2.61E-06 2.36E-11 mr1226_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
vg0309326904 5.96E-06 2.00E-09 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