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Detailed information for vg0617365911:

Variant ID: vg0617365911 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17365911
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCGAGCGGCCTCCTCGCTCCTCGTTCTCGCGACGTCGTGAGGAAACATGATGTCGGGAACGATTCTTGTTGTCTCACGCGCGTCGTGCTTCTCGGCGGC[T/C]
GTTCAGATGGTCGCGGAGATCGCCGGTGCCGCGAGGTGGAGGGGTAGCTCGTGCAGGCGACGTCCGCTGCTCCGGTGGTTCACCGTCGGCACCGCCAGCT

Reverse complement sequence

AGCTGGCGGTGCCGACGGTGAACCACCGGAGCAGCGGACGTCGCCTGCACGAGCTACCCCTCCACCTCGCGGCACCGGCGATCTCCGCGACCATCTGAAC[A/G]
GCCGCCGAGAAGCACGACGCGCGTGAGACAACAAGAATCGTTCCCGACATCATGTTTCCTCACGACGTCGCGAGAACGAGGAGCGAGGAGGCCGCTCGAA

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 67.60% 30.00% 1.84% 0.59% NA
All Indica  2759 98.10% 1.70% 0.18% 0.07% NA
All Japonica  1512 9.90% 88.20% 0.13% 1.72% NA
Aus  269 95.90% 3.00% 1.12% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 95.80% 3.40% 0.51% 0.25% NA
Temperate Japonica  767 3.70% 93.00% 0.00% 3.39% NA
Tropical Japonica  504 22.60% 77.40% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 95.90% 0.83% 0.00% NA
VI/Aromatic  96 28.10% 1.00% 70.83% 0.00% NA
Intermediate  90 57.80% 32.20% 10.00% 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
vg0617365911 T -> C LOC_Os06g30120.1 missense_variant ; p.Cys103Arg; MODERATE nonsynonymous_codon ; C103R Average:72.518; most accessible tissue: Minghui63 flag leaf, score: 84.42 unknown unknown TOLERATED 0.50
vg0617365911 T -> DEL LOC_Os06g30120.1 N frameshift_variant Average:72.518; most accessible tissue: Minghui63 flag leaf, score: 84.42 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)
vg0617365911 T C 0.0 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617365911 NA 4.73E-82 mr1080 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
vg0617365911 NA 1.71E-76 mr1100 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
vg0617365911 NA 2.90E-35 mr1402 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
vg0617365911 NA 7.85E-21 mr1477 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
vg0617365911 2.03E-06 9.97E-42 mr1719 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
vg0617365911 NA 1.65E-16 mr1968 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
vg0617365911 NA 8.22E-20 mr1165_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
vg0617365911 NA 1.43E-31 mr1477_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
vg0617365911 NA 1.97E-09 mr1478_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
vg0617365911 NA 6.72E-21 mr1968_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
vg0617365911 NA 5.14E-23 mr1971_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
vg0617365911 1.94E-06 1.94E-06 mr1971_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