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Detailed information for vg0105512728:

Variant ID: vg0105512728 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5512728
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.26, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TGCCTTCAGGCCCTTCGAATTAACAGAGTTCACCGGAGGGCTTGAAGGGATATCAAAATCTGCCTTCTGCTTGTTGGCCTTTTCCTTATCAATCTGAAGC[G/A]
AGGAGCGGGCTGTTGGCAAGCTCACAGAGTGCTTGAACGCAGCCACTGCATCCTCGTCCCGGTTAACAGGCATCGACACAGACTTCCCCATACTAATAAA

Reverse complement sequence

TTTATTAGTATGGGGAAGTCTGTGTCGATGCCTGTTAACCGGGACGAGGATGCAGTGGCTGCGTTCAAGCACTCTGTGAGCTTGCCAACAGCCCGCTCCT[C/T]
GCTTCAGATTGATAAGGAAAAGGCCAACAAGCAGAAGGCAGATTTTGATATCCCTTCAAGCCCTCCGGTGAACTCTGTTAATTCGAAGGGCCTGAAGGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.20% 47.60% 0.11% 0.04% NA
All Indica  2759 77.60% 22.20% 0.11% 0.04% NA
All Japonica  1512 2.20% 97.80% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 51.30% 48.40% 0.17% 0.17% NA
Indica II  465 75.70% 24.30% 0.00% 0.00% NA
Indica III  913 95.60% 4.40% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 21.90% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 3.20% 96.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 90.60% 1.04% 1.04% NA
Intermediate  90 43.30% 55.60% 1.11% 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
vg0105512728 G -> A LOC_Os01g10450.1 missense_variant ; p.Ser75Leu; MODERATE nonsynonymous_codon ; S75L Average:79.559; most accessible tissue: Minghui63 flag leaf, score: 87.189 benign -0.154 TOLERATED 0.27
vg0105512728 G -> A LOC_Os01g10450.2 missense_variant ; p.Ser75Leu; MODERATE nonsynonymous_codon ; S75L Average:79.559; most accessible tissue: Minghui63 flag leaf, score: 87.189 benign -0.154 TOLERATED 0.27
vg0105512728 G -> DEL LOC_Os01g10450.1 N frameshift_variant Average:79.559; most accessible tissue: Minghui63 flag leaf, score: 87.189 N N N N
vg0105512728 G -> DEL LOC_Os01g10450.2 N frameshift_variant Average:79.559; most accessible tissue: Minghui63 flag leaf, score: 87.189 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)
vg0105512728 G A 0.01 -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
vg0105512728 NA 4.83E-06 mr1072 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
vg0105512728 NA 4.78E-07 mr1190 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
vg0105512728 NA 6.43E-07 mr1445 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
vg0105512728 NA 2.94E-10 mr1498 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
vg0105512728 NA 4.23E-11 mr1498 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
vg0105512728 NA 2.69E-07 mr1545 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
vg0105512728 9.01E-07 9.00E-07 mr1545 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
vg0105512728 NA 1.73E-07 mr1633 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
vg0105512728 NA 9.55E-06 mr1633 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
vg0105512728 NA 1.85E-08 mr1659 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
vg0105512728 NA 1.09E-10 mr1683 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
vg0105512728 4.40E-06 NA mr1769 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
vg0105512728 NA 2.30E-06 mr1795 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
vg0105512728 NA 3.83E-16 mr1909 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
vg0105512728 NA 8.88E-06 mr1909 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
vg0105512728 NA 6.87E-12 mr1921 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
vg0105512728 NA 7.01E-10 mr1925 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
vg0105512728 NA 5.93E-08 mr1951 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
vg0105512728 NA 3.55E-09 mr1951 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
vg0105512728 NA 7.75E-09 mr1498_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
vg0105512728 NA 1.37E-07 mr1925_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
vg0105512728 NA 2.03E-06 mr1951_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
vg0105512728 NA 4.93E-07 mr1951_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