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Detailed information for vg0128940445:

Variant ID: vg0128940445 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28940445
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGGCCGGTGGCCATCTCGATGATGGTGCAGCCGAGGGCCCAGACATCGGCCGCCGGCCCCTGCTCCTCCCCGCGCGCCACCTCCGGCGCCATGAACGC[C/A]
GGCGTGCCGCCGATCGGCCCCGCCGAGTCCATGACCCTCGCGCACCCGAAGTCCGTGAGCCTCGCCCGGCCGTCGCTCCCGATCACGACGTTCCTCGCCT

Reverse complement sequence

AGGCGAGGAACGTCGTGATCGGGAGCGACGGCCGGGCGAGGCTCACGGACTTCGGGTGCGCGAGGGTCATGGACTCGGCGGGGCCGATCGGCGGCACGCC[G/T]
GCGTTCATGGCGCCGGAGGTGGCGCGCGGGGAGGAGCAGGGGCCGGCGGCCGATGTCTGGGCCCTCGGCTGCACCATCATCGAGATGGCCACCGGCCGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.50% 11.90% 0.51% 0.15% NA
All Indica  2759 89.30% 10.60% 0.14% 0.00% NA
All Japonica  1512 98.40% 0.20% 0.99% 0.40% NA
Aus  269 13.40% 85.10% 1.49% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 83.10% 16.80% 0.11% 0.00% NA
Indica Intermediate  786 86.60% 13.00% 0.38% 0.00% NA
Temperate Japonica  767 97.70% 0.00% 1.69% 0.65% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.20% 0.83% 0.41% NA
VI/Aromatic  96 65.60% 33.30% 1.04% 0.00% NA
Intermediate  90 92.20% 6.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0128940445 C -> A LOC_Os01g50410.1 synonymous_variant ; p.Pro161Pro; LOW synonymous_codon Average:95.304; most accessible tissue: Zhenshan97 flower, score: 99.248 N N N N
vg0128940445 C -> DEL LOC_Os01g50410.1 N frameshift_variant Average:95.304; most accessible tissue: Zhenshan97 flower, score: 99.248 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)
vg0128940445 C A -0.02 -0.02 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128940445 NA 1.74E-09 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
vg0128940445 NA 9.97E-06 mr1060_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
vg0128940445 NA 3.11E-12 mr1193_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
vg0128940445 NA 9.78E-06 mr1277_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
vg0128940445 NA 1.60E-08 mr1327_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
vg0128940445 NA 7.83E-06 mr1344_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
vg0128940445 NA 1.54E-06 mr1358_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
vg0128940445 NA 8.47E-10 mr1388_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
vg0128940445 NA 2.07E-09 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
vg0128940445 5.68E-06 1.94E-09 mr1511_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
vg0128940445 4.15E-06 9.15E-07 mr1511_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
vg0128940445 NA 8.41E-06 mr1624_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
vg0128940445 NA 1.41E-06 mr1740_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
vg0128940445 NA 8.24E-18 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