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Detailed information for vg0429839310:

Variant ID: vg0429839310 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29839310
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCCTAACAGTTAGAACTACATTTAGTGAAAGATATGTTTATACTCCGTCCTAAAATTAGTGTGCAGTTTTATTTTAAAACGGAGGGAGTAATTCCTTA[G/A]
CAGAAATCTCATGCACGGCACATTAACTTGCAGACCCACATGCCAGAAGGAAAACAATGAGAAGTAAATAGTGATAATTTTTGGCTAATGTATGGTGAAG

Reverse complement sequence

CTTCACCATACATTAGCCAAAAATTATCACTATTTACTTCTCATTGTTTTCCTTCTGGCATGTGGGTCTGCAAGTTAATGTGCCGTGCATGAGATTTCTG[C/T]
TAAGGAATTACTCCCTCCGTTTTAAAATAAAACTGCACACTAATTTTAGGACGGAGTATAAACATATCTTTCACTAAATGTAGTTCTAACTGTTAGGAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.50% 47.10% 0.21% 0.21% NA
All Indica  2759 47.20% 52.30% 0.25% 0.29% NA
All Japonica  1512 70.70% 29.20% 0.00% 0.07% NA
Aus  269 23.80% 76.20% 0.00% 0.00% NA
Indica I  595 76.10% 23.50% 0.17% 0.17% NA
Indica II  465 15.70% 83.40% 0.65% 0.22% NA
Indica III  913 46.70% 53.10% 0.00% 0.22% NA
Indica Intermediate  786 44.50% 54.60% 0.38% 0.51% NA
Temperate Japonica  767 53.20% 46.70% 0.00% 0.13% NA
Tropical Japonica  504 93.80% 6.20% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 22.00% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 95.80% 2.08% 0.00% NA
Intermediate  90 48.90% 48.90% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429839310 G -> DEL N N silent_mutation Average:67.967; most accessible tissue: Callus, score: 94.099 N N N N
vg0429839310 G -> A LOC_Os04g50030-LOC_Os04g50040 intergenic_region ; MODIFIER silent_mutation Average:67.967; most accessible tissue: Callus, score: 94.099 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)
vg0429839310 G A 0.0 0.0 0.0 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429839310 NA 1.85E-06 mr1138 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
vg0429839310 NA 6.96E-10 mr1169 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
vg0429839310 NA 3.67E-12 mr1174 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
vg0429839310 NA 3.86E-09 mr1347 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
vg0429839310 NA 8.67E-08 mr1406 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
vg0429839310 NA 1.22E-06 mr1062_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
vg0429839310 8.41E-07 5.44E-10 mr1174_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
vg0429839310 1.79E-06 2.46E-16 mr1174_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
vg0429839310 NA 1.52E-06 mr1243_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
vg0429839310 1.24E-06 NA mr1347_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
vg0429839310 1.55E-06 3.92E-17 mr1347_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
vg0429839310 4.13E-06 1.80E-06 mr1406_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
vg0429839310 NA 3.22E-08 mr1406_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
vg0429839310 NA 1.10E-07 mr1539_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
vg0429839310 NA 1.48E-08 mr1540_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
vg0429839310 NA 2.04E-08 mr1732_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