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Detailed information for vg0134886877:

Variant ID: vg0134886877 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34886877
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGTGGACACGCGGCCATGCGGCTATCCAACCAGATGCGCTGATGTACAAACACGTACTCCCTCCTAAAAAAAAAAAAAGTTTCCGTGCCCAATATTTAA[C/T]
CGTACGTCTTATTTAAAAAAATTATAAAAAATTAAAAAAACAAGTCACGCATAAAATATTAATTATGTTTTATCATGTAACAACAATAAAAACACGAATT

Reverse complement sequence

AATTCGTGTTTTTATTGTTGTTACATGATAAAACATAATTAATATTTTATGCGTGACTTGTTTTTTTAATTTTTTATAATTTTTTTAAATAAGACGTACG[G/A]
TTAAATATTGGGCACGGAAACTTTTTTTTTTTTTAGGAGGGAGTACGTGTTTGTACATCAGCGCATCTGGTTGGATAGCCGCATGGCCGCGTGTCCACGG

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 70.80% 13.70% 2.16% 13.35% NA
All Indica  2759 75.40% 22.40% 1.78% 0.47% NA
All Japonica  1512 70.60% 1.40% 1.19% 26.79% NA
Aus  269 41.60% 0.00% 9.29% 49.07% NA
Indica I  595 82.50% 14.60% 2.86% 0.00% NA
Indica II  465 26.00% 69.50% 4.30% 0.22% NA
Indica III  913 98.50% 1.30% 0.00% 0.22% NA
Indica Intermediate  786 72.40% 24.80% 1.53% 1.27% NA
Temperate Japonica  767 72.80% 1.30% 1.30% 24.64% NA
Tropical Japonica  504 85.50% 1.80% 0.40% 12.30% NA
Japonica Intermediate  241 32.80% 0.80% 2.49% 63.90% NA
VI/Aromatic  96 19.80% 2.10% 7.29% 70.83% NA
Intermediate  90 72.20% 10.00% 3.33% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0134886877 C -> T LOC_Os01g60309.1 upstream_gene_variant ; 1436.0bp to feature; MODIFIER silent_mutation Average:87.18; most accessible tissue: Minghui63 young leaf, score: 95.066 N N N N
vg0134886877 C -> T LOC_Os01g60290.1 intron_variant ; MODIFIER silent_mutation Average:87.18; most accessible tissue: Minghui63 young leaf, score: 95.066 N N N N
vg0134886877 C -> DEL N N silent_mutation Average:87.18; most accessible tissue: Minghui63 young leaf, score: 95.066 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)
vg0134886877 C T -0.09 -0.09 -0.05 -0.09 -0.1 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134886877 NA 6.94E-20 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
vg0134886877 NA 1.06E-14 Plant_height 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
vg0134886877 NA 3.80E-09 mr1003 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
vg0134886877 NA 7.57E-06 mr1011 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
vg0134886877 NA 7.67E-09 mr1051 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
vg0134886877 NA 6.25E-09 mr1163 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
vg0134886877 NA 5.43E-06 mr1192 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
vg0134886877 NA 1.83E-07 mr1192 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
vg0134886877 NA 3.41E-06 mr1274 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
vg0134886877 NA 3.25E-06 mr1051_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
vg0134886877 NA 5.55E-06 mr1268_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
vg0134886877 NA 7.57E-06 mr1274_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
vg0134886877 NA 1.51E-07 mr1302_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
vg0134886877 NA 1.32E-11 mr1319_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
vg0134886877 NA 4.53E-07 mr1319_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
vg0134886877 NA 5.33E-15 mr1327_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
vg0134886877 NA 2.22E-14 mr1327_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
vg0134886877 NA 1.23E-13 mr1330_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
vg0134886877 NA 2.68E-07 mr1330_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
vg0134886877 NA 1.42E-19 mr1352_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
vg0134886877 NA 8.40E-07 mr1378_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
vg0134886877 NA 9.37E-06 mr1460_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
vg0134886877 NA 1.43E-07 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