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Detailed information for vg1019392093:

Variant ID: vg1019392093 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19392093
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTACGAGCACACGAGGGAGGCGGTGAGATCGCTGGATCAGGAGAAAGGATTGGTGCGAAAGCACAATTTTACCCTCCCACCAACAGAACACAATCGGTA[C/T]
CTCCTTTCGCGGGGACGCGGTACCACCAGGTATCGAGCAATTCCAGCCGTTAGATTGCGCCAGATCGAGTGCCAGGATATGGTACAGCCTCCCCTCAAGG

Reverse complement sequence

CCTTGAGGGGAGGCTGTACCATATCCTGGCACTCGATCTGGCGCAATCTAACGGCTGGAATTGCTCGATACCTGGTGGTACCGCGTCCCCGCGAAAGGAG[G/A]
TACCGATTGTGTTCTGTTGGTGGGAGGGTAAAATTGTGCTTTCGCACCAATCCTTTCTCCTGATCCAGCGATCTCACCGCCTCCCTCGTGTGCTCGTACG

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 44.60% 25.60% 0.25% 29.52% NA
All Indica  2759 62.60% 2.10% 0.25% 35.09% NA
All Japonica  1512 22.30% 72.50% 0.07% 5.16% NA
Aus  269 4.50% 2.20% 0.74% 92.57% NA
Indica I  595 93.80% 1.80% 0.00% 4.37% NA
Indica II  465 58.30% 1.30% 0.22% 40.22% NA
Indica III  913 46.80% 2.20% 0.11% 50.93% NA
Indica Intermediate  786 59.90% 2.50% 0.64% 36.90% NA
Temperate Japonica  767 2.90% 94.90% 0.13% 2.09% NA
Tropical Japonica  504 57.70% 32.50% 0.00% 9.72% NA
Japonica Intermediate  241 10.00% 84.60% 0.00% 5.39% NA
VI/Aromatic  96 2.10% 28.10% 1.04% 68.75% NA
Intermediate  90 35.60% 25.60% 1.11% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019392093 C -> T LOC_Os10g36270.1 5_prime_UTR_variant ; 2184.0bp to feature; MODIFIER silent_mutation Average:45.374; most accessible tissue: Zhenshan97 root, score: 92.725 N N N N
vg1019392093 C -> DEL N N silent_mutation Average:45.374; most accessible tissue: Zhenshan97 root, score: 92.725 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)
vg1019392093 C T 0.02 -0.01 -0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019392093 NA 5.09E-07 mr1308 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
vg1019392093 NA 2.71E-06 mr1509 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
vg1019392093 NA 8.49E-08 mr1551 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
vg1019392093 NA 2.03E-16 mr1771 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
vg1019392093 NA 3.75E-13 mr1784 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
vg1019392093 NA 1.33E-07 mr1805 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
vg1019392093 NA 6.96E-07 mr1942 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
vg1019392093 NA 1.14E-06 mr1248_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
vg1019392093 9.01E-07 NA mr1558_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
vg1019392093 NA 7.35E-13 mr1771_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
vg1019392093 NA 2.28E-13 mr1784_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
vg1019392093 NA 6.48E-10 mr1800_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
vg1019392093 NA 1.15E-08 mr1805_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
vg1019392093 NA 1.79E-07 mr1817_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
vg1019392093 NA 1.12E-12 mr1862_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