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Detailed information for vg1127573927:

Variant ID: vg1127573927 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27573927
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCAGCCGCTGCAGGCAGAGGCGTTCGCGTCGCCGCGGCAGAGCGCGACGGCGTAGACGGTGTCCGGGGCGGCGCCGCGGGAGCCCTTGGCGAATAGGG[C/A]
GCCGCTGCTGGAGTCGCCGCTTACGACAAGGAATGATGAGGAGAGAAGGCTGTCGAGGTTGGATTGGTAGATGCTGTTCGCCGTGTATTTGCTGCTGCCG

Reverse complement sequence

CGGCAGCAGCAAATACACGGCGAACAGCATCTACCAATCCAACCTCGACAGCCTTCTCTCCTCATCATTCCTTGTCGTAAGCGGCGACTCCAGCAGCGGC[G/T]
CCCTATTCGCCAAGGGCTCCCGCGGCGCCGCCCCGGACACCGTCTACGCCGTCGCGCTCTGCCGCGGCGACGCGAACGCCTCTGCCTGCAGCGGCTGCGT

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 50.40% 40.00% 0.40% 9.20% NA
All Indica  2759 46.50% 44.80% 0.47% 8.19% NA
All Japonica  1512 61.60% 32.10% 0.20% 6.02% NA
Aus  269 17.10% 38.70% 1.12% 43.12% NA
Indica I  595 65.90% 13.60% 0.84% 19.66% NA
Indica II  465 83.20% 15.70% 0.43% 0.65% NA
Indica III  913 14.50% 81.30% 0.00% 4.27% NA
Indica Intermediate  786 47.50% 43.30% 0.76% 8.52% NA
Temperate Japonica  767 75.70% 13.00% 0.26% 10.95% NA
Tropical Japonica  504 37.90% 61.30% 0.00% 0.79% NA
Japonica Intermediate  241 66.40% 32.00% 0.41% 1.24% NA
VI/Aromatic  96 65.60% 34.40% 0.00% 0.00% NA
Intermediate  90 64.40% 33.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127573927 C -> A LOC_Os11g45540.1 missense_variant ; p.Ala63Ser; MODERATE nonsynonymous_codon ; A63F Average:81.313; most accessible tissue: Minghui63 young leaf, score: 88.372 unknown unknown TOLERATED 0.47
vg1127573927 C -> DEL LOC_Os11g45540.1 N frameshift_variant Average:81.313; most accessible tissue: Minghui63 young leaf, score: 88.372 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)
vg1127573927 C A 0.02 -0.01 0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127573927 NA 1.30E-08 mr1063 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
vg1127573927 4.34E-07 NA mr1133 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
vg1127573927 5.83E-07 1.62E-16 mr1133 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
vg1127573927 NA 2.71E-06 mr1526 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
vg1127573927 5.71E-07 NA mr1667 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
vg1127573927 2.57E-06 4.42E-10 mr1667 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
vg1127573927 NA 1.50E-09 mr1063_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
vg1127573927 NA 2.56E-11 mr1065_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
vg1127573927 NA 2.64E-10 mr1091_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
vg1127573927 NA 2.23E-06 mr1094_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
vg1127573927 NA 3.13E-07 mr1096_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
vg1127573927 NA 1.58E-06 mr1111_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
vg1127573927 NA 1.60E-07 mr1125_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
vg1127573927 5.52E-07 7.68E-16 mr1133_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
vg1127573927 NA 8.86E-07 mr1144_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
vg1127573927 7.52E-06 4.35E-10 mr1667_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