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Detailed information for vg0430617282:

Variant ID: vg0430617282 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30617282
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTTCATGTTTATAGATATGATTAAACTTTCTTTAAGGACAGAGGGGTACTCTCTTGTGAGTATTTGAGAGTAGAGAATTAGAGAAGATTGAGAAGATA[T/C]
ACAAACGAGATACTTAAAAGTTATATTAATATATTTTTTTAAATTAACTTTGATATATTCGTTTAGCTATTCGAGGAATGTGTATACAAAAAACGAAGGA

Reverse complement sequence

TCCTTCGTTTTTTGTATACACATTCCTCGAATAGCTAAACGAATATATCAAAGTTAATTTAAAAAAATATATTAATATAACTTTTAAGTATCTCGTTTGT[A/G]
TATCTTCTCAATCTTCTCTAATTCTCTACTCTCAAATACTCACAAGAGAGTACCCCTCTGTCCTTAAAGAAAGTTTAATCATATCTATAAACATGAACAA

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 86.90% 12.90% 0.21% 0.00% NA
All Indica  2759 98.90% 1.00% 0.07% 0.00% NA
All Japonica  1512 61.80% 37.60% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.30% 0.34% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 36.00% 63.10% 0.91% 0.00% NA
Tropical Japonica  504 93.70% 6.30% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 0.00% 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
vg0430617282 T -> C LOC_Os04g51680.1 upstream_gene_variant ; 1107.0bp to feature; MODIFIER silent_mutation Average:86.981; most accessible tissue: Minghui63 panicle, score: 97.04 N N N N
vg0430617282 T -> C LOC_Os04g51690.1 downstream_gene_variant ; 3878.0bp to feature; MODIFIER silent_mutation Average:86.981; most accessible tissue: Minghui63 panicle, score: 97.04 N N N N
vg0430617282 T -> C LOC_Os04g51680-LOC_Os04g51690 intergenic_region ; MODIFIER silent_mutation Average:86.981; most accessible tissue: Minghui63 panicle, score: 97.04 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)
vg0430617282 T C -0.01 -0.02 -0.01 -0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430617282 NA 3.44E-06 mr1057 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
vg0430617282 NA 4.12E-12 mr1182 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
vg0430617282 NA 2.59E-10 mr1282 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
vg0430617282 NA 1.76E-11 mr1650 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
vg0430617282 NA 1.23E-09 mr1658 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
vg0430617282 NA 1.07E-06 mr1677 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
vg0430617282 NA 6.46E-10 mr1002_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
vg0430617282 1.64E-06 2.35E-07 mr1057_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
vg0430617282 NA 2.20E-07 mr1057_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
vg0430617282 NA 5.54E-14 mr1182_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
vg0430617282 NA 2.85E-06 mr1182_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
vg0430617282 NA 1.09E-12 mr1282_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
vg0430617282 NA 9.21E-06 mr1446_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
vg0430617282 5.48E-08 NA mr1530_2 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
vg0430617282 4.74E-06 6.70E-14 mr1530_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