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Detailed information for vg0102821219:

Variant ID: vg0102821219 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2821219
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGAGCTACTACTATTTCTTTTTGCTCTAAAGTCTATACAAACATGTTAATGTCTTAGCGTATGACCTCATCAACCGTCCGGCCTTCCACGGTGAATCG[C/T]
TAAAATGGTATAACACCTGTTGTTTGTCAATAGCATTATCACAGCATAAAGCAATTGAACCAGTCGCATGAACCTCTATTTCTTTTTTTCCCAAATTAGA

Reverse complement sequence

TCTAATTTGGGAAAAAAAGAAATAGAGGTTCATGCGACTGGTTCAATTGCTTTATGCTGTGATAATGCTATTGACAAACAACAGGTGTTATACCATTTTA[G/A]
CGATTCACCGTGGAAGGCCGGACGGTTGATGAGGTCATACGCTAAGACATTAACATGTTTGTATAGACTTTAGAGCAAAAAGAAATAGTAGTAGCTCGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 1.10% 2.52% 0.30% NA
All Indica  2759 95.00% 1.20% 3.30% 0.51% NA
All Japonica  1512 97.50% 1.10% 1.39% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 98.20% 0.80% 1.01% 0.00% NA
Indica II  465 97.20% 0.20% 2.37% 0.22% NA
Indica III  913 93.10% 1.40% 4.49% 0.99% NA
Indica Intermediate  786 93.40% 1.90% 4.20% 0.51% NA
Temperate Japonica  767 98.80% 0.70% 0.52% 0.00% NA
Tropical Japonica  504 94.60% 2.00% 3.37% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 0.00% 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
vg0102821219 C -> T LOC_Os01g05880.1 upstream_gene_variant ; 4818.0bp to feature; MODIFIER silent_mutation Average:97.182; most accessible tissue: Callus, score: 99.792 N N N N
vg0102821219 C -> T LOC_Os01g05890.1 upstream_gene_variant ; 2322.0bp to feature; MODIFIER silent_mutation Average:97.182; most accessible tissue: Callus, score: 99.792 N N N N
vg0102821219 C -> T LOC_Os01g05900.1 intron_variant ; MODIFIER silent_mutation Average:97.182; most accessible tissue: Callus, score: 99.792 N N N N
vg0102821219 C -> DEL N N silent_mutation Average:97.182; most accessible tissue: Callus, score: 99.792 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)
vg0102821219 C T -0.01 -0.02 -0.03 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102821219 7.80E-06 7.80E-06 mr1542_2 Jap_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
vg0102821219 NA 2.72E-06 mr1680_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
vg0102821219 NA 1.19E-08 mr1742_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
vg0102821219 NA 1.58E-09 mr1769_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
vg0102821219 NA 1.09E-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