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Detailed information for vg0608085803:

Variant ID: vg0608085803 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8085803
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTGGTGTGATATATGATTGATATCATGAGTGCCCTACCTCAATCCATTTATCAACTTTATATATATATATATATATATATATATATGCACGATTGA[C/T]
TAGTCCATGATTTGCCTGTTAATTGCGTCTGTTTTTTTTATATATTTAAGGATGATTTTATAGCTCTTGACTGAAGCAACAGAGAACCACCACATTGTAT

Reverse complement sequence

ATACAATGTGGTGGTTCTCTGTTGCTTCAGTCAAGAGCTATAAAATCATCCTTAAATATATAAAAAAAACAGACGCAATTAACAGGCAAATCATGGACTA[G/A]
TCAATCGTGCATATATATATATATATATATATATATATAAAGTTGATAAATGGATTGAGGTAGGGCACTCATGATATCAATCATATATCACACCAAAAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.40% 10.60% 0.55% 23.47% NA
All Indica  2759 98.30% 0.10% 0.11% 1.45% NA
All Japonica  1512 1.90% 32.50% 0.86% 64.75% NA
Aus  269 93.30% 0.00% 0.00% 6.69% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.40% 0.00% 0.00% 2.58% NA
Indica III  913 98.40% 0.00% 0.11% 1.53% NA
Indica Intermediate  786 97.80% 0.10% 0.25% 1.78% NA
Temperate Japonica  767 1.60% 57.40% 0.26% 40.81% NA
Tropical Japonica  504 1.60% 1.00% 0.99% 96.43% NA
Japonica Intermediate  241 3.30% 19.50% 2.49% 74.69% NA
VI/Aromatic  96 54.20% 0.00% 1.04% 44.79% NA
Intermediate  90 53.30% 4.40% 10.00% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608085803 C -> T LOC_Os06g14430-LOC_Os06g14440 intergenic_region ; MODIFIER silent_mutation Average:69.19; most accessible tissue: Callus, score: 96.618 N N N N
vg0608085803 C -> DEL N N silent_mutation Average:69.19; most accessible tissue: Callus, score: 96.618 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)
vg0608085803 C T -0.18 -0.03 -0.04 0.0 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608085803 1.34E-07 1.17E-08 mr1354 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
vg0608085803 NA 1.65E-06 mr1195_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
vg0608085803 NA 7.83E-06 mr1331_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
vg0608085803 NA 1.34E-06 mr1331_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
vg0608085803 NA 4.02E-08 mr1551_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
vg0608085803 7.52E-08 NA mr1679_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
vg0608085803 NA 2.44E-06 mr1761_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
vg0608085803 2.90E-08 NA mr1829_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
vg0608085803 9.76E-07 NA mr1902_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