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Detailed information for vg1102424189:

Variant ID: vg1102424189 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2424189
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCTGAACTCCGACAGGTGCGCCGACTTGTGCCCCTTGATGAACCTTCATCAAATTTAATTAATCAAAGTTCAATTAACTAAGCTAATCACACATATAA[T/C]
TAACGTTATCAACTACGCAGATATAAATAGTTAAGGCATAGTTAGTTCCCAAATTTTTTTCCTAAAAACATCACATCGAATCTTTGAACACATGGTTAGA

Reverse complement sequence

TCTAACCATGTGTTCAAAGATTCGATGTGATGTTTTTAGGAAAAAAATTTGGGAACTAACTATGCCTTAACTATTTATATCTGCGTAGTTGATAACGTTA[A/G]
TTATATGTGTGATTAGCTTAGTTAATTGAACTTTGATTAATTAAATTTGATGAAGGTTCATCAAGGGGCACAAGTCGGCGCACCTGTCGGAGTTCAGGGA

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 96.90% 3.00% 0.11% 0.00% NA
All Indica  2759 95.00% 4.90% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 83.00% 16.80% 0.22% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 3.90% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1102424189 T -> C LOC_Os11g05394.1 upstream_gene_variant ; 826.0bp to feature; MODIFIER silent_mutation Average:92.087; most accessible tissue: Minghui63 flag leaf, score: 96.501 N N N N
vg1102424189 T -> C LOC_Os11g05394.2 upstream_gene_variant ; 824.0bp to feature; MODIFIER silent_mutation Average:92.087; most accessible tissue: Minghui63 flag leaf, score: 96.501 N N N N
vg1102424189 T -> C LOC_Os11g05400.1 intron_variant ; MODIFIER silent_mutation Average:92.087; most accessible tissue: Minghui63 flag leaf, score: 96.501 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)
vg1102424189 T C 0.03 0.03 0.03 -0.02 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102424189 NA 2.40E-06 mr1077 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
vg1102424189 NA 2.49E-06 mr1120 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
vg1102424189 NA 1.20E-07 mr1415 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
vg1102424189 2.89E-06 2.89E-06 mr1424 Ind_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
vg1102424189 NA 1.20E-07 mr1567 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
vg1102424189 NA 3.62E-06 mr1715 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
vg1102424189 NA 5.57E-06 mr1806 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
vg1102424189 1.17E-07 1.17E-07 mr1992 Ind_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
vg1102424189 NA 3.93E-07 mr1806_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
vg1102424189 NA 8.60E-12 mr1828_2 Ind_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
vg1102424189 NA 8.72E-06 mr1938_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