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Detailed information for vg0822370256:

Variant ID: vg0822370256 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22370256
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATGAACGCGTCGAACATCTTGCCCACCTTCTTCATCCGCCGCACGTACCCCTGCAGGTCCATCCAGTCCACCCACGGGATCCAGTCGCCGACGTTGAG[G/C]
ACGCCGTTGAGCAGGAGGAGCTCGTCCAGCATCCACTTGAACTCCGACAGCGTCGACACGGGCCCCTCCGCCGCGTCCGCGCCCTCGCCGAAGAACCGCT

Reverse complement sequence

AGCGGTTCTTCGGCGAGGGCGCGGACGCGGCGGAGGGGCCCGTGTCGACGCTGTCGGAGTTCAAGTGGATGCTGGACGAGCTCCTCCTGCTCAACGGCGT[C/G]
CTCAACGTCGGCGACTGGATCCCGTGGGTGGACTGGATGGACCTGCAGGGGTACGTGCGGCGGATGAAGAAGGTGGGCAAGATGTTCGACGCGTTCATGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.10% 34.60% 0.11% 0.19% NA
All Indica  2759 98.00% 1.60% 0.11% 0.29% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.07% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.34% 0.17% NA
Indica II  465 97.80% 1.30% 0.00% 0.86% NA
Indica III  913 98.90% 1.00% 0.00% 0.11% NA
Indica Intermediate  786 96.10% 3.60% 0.13% 0.25% NA
Temperate Japonica  767 1.30% 98.60% 0.00% 0.13% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 56.70% 41.10% 2.22% 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
vg0822370256 G -> C LOC_Os08g35510.1 synonymous_variant ; p.Val228Val; LOW synonymous_codon Average:89.168; most accessible tissue: Minghui63 flag leaf, score: 93.28 N N N N
vg0822370256 G -> DEL LOC_Os08g35510.1 N frameshift_variant Average:89.168; most accessible tissue: Minghui63 flag leaf, score: 93.28 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)
vg0822370256 G C 0.0 0.0 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822370256 NA 7.08E-66 mr1027 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
vg0822370256 NA 7.86E-45 mr1194 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
vg0822370256 NA 2.92E-31 mr1243 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
vg0822370256 NA 1.22E-26 mr1309 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
vg0822370256 NA 4.68E-46 mr1591 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
vg0822370256 NA 8.45E-57 mr1594 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
vg0822370256 NA 2.02E-53 mr1599 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
vg0822370256 NA 1.27E-20 mr1627 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
vg0822370256 NA 4.49E-28 mr1793 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
vg0822370256 NA 5.54E-35 mr1828 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
vg0822370256 NA 5.24E-34 mr1932 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
vg0822370256 NA 4.78E-16 mr1968 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
vg0822370256 NA 1.97E-52 mr1194_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
vg0822370256 NA 1.43E-51 mr1480_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
vg0822370256 NA 3.83E-15 mr1578_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
vg0822370256 NA 2.65E-31 mr1913_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
vg0822370256 NA 1.68E-21 mr1968_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