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Detailed information for vg1107886187:

Variant ID: vg1107886187 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7886187
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTGTATATGAGTCGGGTTTTAAATCCGTTCGCTTTTAGAAATACAAAATCTATATTTGAGACGGGTTTTAAGTTCTTTCGCTTTTAAAAATATAGAAG[G/A]
AATCGTATAAGAAATCTTTTCAAAAACCTCGCATATTAACTTGAGACAATTGGACTCCTAATTACAGCTCATGATTTTCTAACAAACTATTTATCCAAGT

Reverse complement sequence

ACTTGGATAAATAGTTTGTTAGAAAATCATGAGCTGTAATTAGGAGTCCAATTGTCTCAAGTTAATATGCGAGGTTTTTGAAAAGATTTCTTATACGATT[C/T]
CTTCTATATTTTTAAAAGCGAAAGAACTTAAAACCCGTCTCAAATATAGATTTTGTATTTCTAAAAGCGAACGGATTTAAAACCCGACTCATATACAGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.10% 6.50% 2.43% 0.00% NA
All Indica  2759 99.60% 0.00% 0.40% 0.00% NA
All Japonica  1512 74.20% 19.60% 6.15% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 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 98.90% 0.00% 1.15% 0.00% NA
Temperate Japonica  767 91.70% 2.70% 5.61% 0.00% NA
Tropical Japonica  504 46.40% 47.80% 5.75% 0.00% NA
Japonica Intermediate  241 76.80% 14.50% 8.71% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 7.80% 6.67% 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
vg1107886187 G -> A LOC_Os11g14140-LOC_Os11g14150 intergenic_region ; MODIFIER silent_mutation Average:74.185; most accessible tissue: Minghui63 flower, score: 90.757 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)
vg1107886187 G A 0.02 0.02 0.02 0.0 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107886187 NA 2.21E-10 mr1016 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
vg1107886187 NA 7.53E-06 mr1236 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
vg1107886187 NA 2.50E-06 mr1248 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
vg1107886187 NA 2.82E-07 mr1543 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
vg1107886187 NA 3.89E-06 mr1742 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
vg1107886187 3.88E-10 1.87E-20 mr1871 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
vg1107886187 NA 1.82E-08 mr1871 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
vg1107886187 NA 1.68E-09 mr1019_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
vg1107886187 3.66E-06 1.29E-19 mr1042_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
vg1107886187 NA 3.24E-12 mr1055_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
vg1107886187 NA 1.31E-10 mr1680_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
vg1107886187 NA 2.11E-13 mr1742_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
vg1107886187 1.41E-10 1.87E-26 mr1871_2 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
vg1107886187 NA 2.81E-08 mr1871_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