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Detailed information for vg0131668403:

Variant ID: vg0131668403 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31668403
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AAGTTATCTGGAGTTACTCAACGATTTGATGAGCTGCTGGGGTACGAAGAGCCGGGTCTTCCAGCTAGCTTCATAAGGTGGTGAGCGATATGTATTCGAA[G/A]
CCTCACCCCTTCTAATTATTTGTATAATAGGCCATTTCCTAATATTCACGTCTTTATTTGATGAACCGCTGTACGCCTGTACCTAGTGCTCCATTGACTA

Reverse complement sequence

TAGTCAATGGAGCACTAGGTACAGGCGTACAGCGGTTCATCAAATAAAGACGTGAATATTAGGAAATGGCCTATTATACAAATAATTAGAAGGGGTGAGG[C/T]
TTCGAATACATATCGCTCACCACCTTATGAAGCTAGCTGGAAGACCCGGCTCTTCGTACCCCAGCAGCTCATCAAATCGTTGAGTAACTCCAGATAACTT

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 60.90% 36.30% 1.61% 1.23% NA
All Indica  2759 47.80% 52.20% 0.07% 0.00% NA
All Japonica  1512 88.10% 3.30% 4.76% 3.84% NA
Aus  269 32.70% 67.30% 0.00% 0.00% NA
Indica I  595 50.30% 49.60% 0.17% 0.00% NA
Indica II  465 4.90% 95.10% 0.00% 0.00% NA
Indica III  913 67.70% 32.30% 0.00% 0.00% NA
Indica Intermediate  786 48.10% 51.80% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 0.10% 2.35% 0.39% NA
Tropical Japonica  504 87.50% 7.70% 2.18% 2.58% NA
Japonica Intermediate  241 60.60% 4.10% 17.84% 17.43% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 75.60% 22.20% 2.22% 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
vg0131668403 G -> A LOC_Os01g55070.1 upstream_gene_variant ; 4110.0bp to feature; MODIFIER silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 N N N N
vg0131668403 G -> A LOC_Os01g55080.1 downstream_gene_variant ; 1325.0bp to feature; MODIFIER silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 N N N N
vg0131668403 G -> A LOC_Os01g55090.1 downstream_gene_variant ; 3792.0bp to feature; MODIFIER silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 N N N N
vg0131668403 G -> A LOC_Os01g55090.2 downstream_gene_variant ; 3794.0bp to feature; MODIFIER silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 N N N N
vg0131668403 G -> A LOC_Os01g55070-LOC_Os01g55080 intergenic_region ; MODIFIER silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 N N N N
vg0131668403 G -> DEL N N silent_mutation Average:64.068; most accessible tissue: Minghui63 root, score: 89.247 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)
vg0131668403 G A 0.06 0.0 -0.01 -0.01 0.04 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131668403 NA 1.15E-18 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
vg0131668403 NA 2.93E-07 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
vg0131668403 NA 7.34E-13 mr1010 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
vg0131668403 NA 3.45E-07 mr1010 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
vg0131668403 NA 1.51E-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
vg0131668403 NA 2.31E-06 mr1011 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
vg0131668403 NA 7.49E-06 mr1012 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
vg0131668403 NA 1.36E-07 mr1013 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
vg0131668403 NA 1.24E-07 mr1031 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
vg0131668403 NA 4.05E-06 mr1034 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
vg0131668403 NA 4.33E-08 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
vg0131668403 NA 2.08E-06 mr1056 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
vg0131668403 6.26E-06 2.40E-10 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
vg0131668403 NA 6.60E-06 mr1011_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
vg0131668403 NA 4.80E-07 mr1013_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
vg0131668403 NA 9.89E-07 mr1031_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
vg0131668403 NA 6.65E-07 mr1060_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
vg0131668403 NA 6.36E-09 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
vg0131668403 NA 6.54E-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
vg0131668403 NA 5.04E-11 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
vg0131668403 NA 1.97E-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
vg0131668403 NA 2.04E-14 mr1579_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
vg0131668403 NA 7.55E-22 mr1627_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
vg0131668403 NA 1.08E-06 mr1641_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
vg0131668403 NA 2.41E-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
vg0131668403 NA 1.42E-07 mr1681_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
vg0131668403 NA 4.19E-08 mr1758_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
vg0131668403 NA 1.79E-06 mr1838_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