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Detailed information for vg0804208300:

Variant ID: vg0804208300 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 4208300
Reference Allele: TAlternative Allele: C,TTTTTATCTGAATAAGTTTGC
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.11, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTAATTTATTCACTATTCGGTCGAAAATACATGGCATTTGATATTTTTGGGTCTTTGGAATATAGCTTTTATTATTGTTTTTATCTGAATAAGTTTG[T/C,TTTTTATCTGAATAAGTTTGC]
AAATTTTACTAAGTTCACGAGGATAAGAAATCATCTTTTAAAAAGACAAATCTACATTTACTGTTACTACCTAGCGTTGTTTCCTACTTACGTTTTAAAC

Reverse complement sequence

GTTTAAAACGTAAGTAGGAAACAACGCTAGGTAGTAACAGTAAATGTAGATTTGTCTTTTTAAAAGATGATTTCTTATCCTCGTGAACTTAGTAAAATTT[A/G,GCAAACTTATTCAGATAAAAA]
CAAACTTATTCAGATAAAAACAATAATAAAAGCTATATTCCAAAGACCCAAAAATATCAAATGCCATGTATTTTCGACCGAATAGTGAATAAATTAATAT

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 61.60% 36.20% 0.19% 0.00% TTTTTATCTGAATAAGTTTGC: 1.99%
All Indica  2759 48.80% 47.60% 0.29% 0.00% TTTTTATCTGAATAAGTTTGC: 3.37%
All Japonica  1512 97.80% 2.10% 0.00% 0.00% TTTTTATCTGAATAAGTTTGC: 0.07%
Aus  269 3.00% 97.00% 0.00% 0.00% NA
Indica I  595 64.40% 35.30% 0.00% 0.00% TTTTTATCTGAATAAGTTTGC: 0.34%
Indica II  465 79.40% 20.40% 0.22% 0.00% NA
Indica III  913 29.90% 63.20% 0.22% 0.00% TTTTTATCTGAATAAGTTTGC: 6.68%
Indica Intermediate  786 40.80% 54.70% 0.64% 0.00% TTTTTATCTGAATAAGTTTGC: 3.82%
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.00% 0.00% 0.00% TTTTTATCTGAATAAGTTTGC: 0.20%
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 84.40% 1.04% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0804208300 T -> C LOC_Os08g07490.1 upstream_gene_variant ; 496.0bp to feature; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 N N N N
vg0804208300 T -> C LOC_Os08g07500.1 downstream_gene_variant ; 3143.0bp to feature; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 N N N N
vg0804208300 T -> C LOC_Os08g07490-LOC_Os08g07500 intergenic_region ; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 N N N N
vg0804208300 T -> TTTTTATCTGAATAAGTTTGC LOC_Os08g07490.1 upstream_gene_variant ; 497.0bp to feature; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 N N N N
vg0804208300 T -> TTTTTATCTGAATAAGTTTGC LOC_Os08g07500.1 downstream_gene_variant ; 3142.0bp to feature; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 N N N N
vg0804208300 T -> TTTTTATCTGAATAAGTTTGC LOC_Os08g07490-LOC_Os08g07500 intergenic_region ; MODIFIER silent_mutation Average:69.288; most accessible tissue: Callus, score: 94.802 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)
vg0804208300 T C -0.03 -0.01 -0.01 -0.01 -0.01 -0.02
vg0804208300 T TTTTT* 0.28 -0.18 -0.2 -0.05 -0.24 -0.4

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804208300 NA 2.97E-12 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0804208300 NA 1.21E-16 Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0804208300 NA 9.18E-08 mr1063_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
vg0804208300 NA 9.99E-07 mr1220_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
vg0804208300 NA 3.81E-09 mr1221_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
vg0804208300 NA 7.76E-17 mr1277_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
vg0804208300 NA 9.71E-06 mr1277_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
vg0804208300 NA 1.47E-06 mr1358_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
vg0804208300 NA 7.72E-06 mr1358_2 Ind_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
vg0804208300 NA 9.54E-07 mr1422_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
vg0804208300 NA 7.55E-08 mr1482_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
vg0804208300 NA 4.25E-08 mr1511_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
vg0804208300 NA 8.63E-06 mr1511_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
vg0804208300 NA 1.64E-10 mr1624_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
vg0804208300 NA 1.14E-07 mr1624_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
vg0804208300 NA 5.41E-08 mr1653_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
vg0804208300 NA 1.96E-06 mr1743_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
vg0804208300 NA 5.20E-06 mr1806_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
vg0804208300 NA 1.61E-07 mr1870_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
vg0804208300 NA 1.63E-22 mr1874_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
vg0804208300 NA 1.89E-06 mr1874_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