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Detailed information for vg0429828010:

Variant ID: vg0429828010 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 29828010
Reference Allele: AAlternative Allele: T,ATTTTTTT
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, T: 0.19, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCACGTCCACTGCAAGCAGTGCGCGAACACCATCGTGACACAGTTCACGCAGTTCCCAGGTGTGTGCCTGCTTCAGTACCCCGCAGGCCGCTGCAAAAAA[A/T,ATTTTTTT]
TTTTTTTTGCCGTCTGAATTTGGCGCCTGCGCACGATTTACATTCTGATTAATTGCGTAGTAATAACATGAACAGGAGTCAGAGAGGTGAAATTGGATGG

Reverse complement sequence

CCATCCAATTTCACCTCTCTGACTCCTGTTCATGTTATTACTACGCAATTAATCAGAATGTAAATCGTGCGCAGGCGCCAAATTCAGACGGCAAAAAAAA[T/A,AAAAAAAT]
TTTTTTGCAGCGGCCTGCGGGGTACTGAAGCAGGCACACACCTGGGAACTGCGTGAACTGTGTCACGATGGTGTTCGCGCACTGCTTGCAGTGGACGTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.00% 23.60% 0.34% 0.00% ATTTTTTT: 0.04%
All Indica  2759 60.20% 39.20% 0.58% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 80.00% 19.50% 0.50% 0.00% NA
Indica II  465 29.20% 69.90% 0.86% 0.00% NA
Indica III  913 60.10% 39.40% 0.44% 0.00% NA
Indica Intermediate  786 63.70% 35.60% 0.64% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 18.90% 0.00% 0.00% ATTTTTTT: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429828010 A -> ATTTTTTT LOC_Os04g50000.1 upstream_gene_variant ; 4929.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> ATTTTTTT LOC_Os04g50010.1 upstream_gene_variant ; 4254.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> ATTTTTTT LOC_Os04g50030.1 downstream_gene_variant ; 3226.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> ATTTTTTT LOC_Os04g50020.1 intron_variant ; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> T LOC_Os04g50000.1 upstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> T LOC_Os04g50010.1 upstream_gene_variant ; 4253.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> T LOC_Os04g50030.1 downstream_gene_variant ; 3227.0bp to feature; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 N N N N
vg0429828010 A -> T LOC_Os04g50020.1 intron_variant ; MODIFIER silent_mutation Average:82.368; most accessible tissue: Zhenshan97 root, score: 94.343 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)
vg0429828010 A ATTTT* 0.15 0.02 0.02 0.01 0.09 0.13
vg0429828010 A T -0.01 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429828010 NA 2.05E-13 mr1138 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
vg0429828010 NA 3.88E-07 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
vg0429828010 NA 3.19E-18 mr1169 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
vg0429828010 NA 9.42E-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
vg0429828010 4.53E-06 3.06E-18 mr1174 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
vg0429828010 3.51E-07 1.24E-15 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
vg0429828010 3.94E-06 4.99E-11 mr1347 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
vg0429828010 9.47E-06 1.01E-11 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
vg0429828010 NA 1.52E-07 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
vg0429828010 NA 1.12E-06 mr1354 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
vg0429828010 3.43E-08 7.22E-08 mr1406 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
vg0429828010 3.22E-07 3.46E-11 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
vg0429828010 NA 1.13E-13 mr1138_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
vg0429828010 NA 1.07E-06 mr1138_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
vg0429828010 6.52E-06 4.40E-19 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
vg0429828010 1.03E-07 4.50E-17 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
vg0429828010 4.44E-07 1.81E-16 mr1347_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
vg0429828010 1.97E-07 1.60E-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
vg0429828010 NA 9.62E-07 mr1354_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
vg0429828010 NA 1.83E-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
vg0429828010 NA 1.27E-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
vg0429828010 NA 2.08E-06 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
vg0429828010 NA 1.63E-06 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