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Detailed information for vg0814660415:

Variant ID: vg0814660415 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14660415
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGAGCTGCAGGGTGTTGCCGATAAAATAGAGAATTTATCCAGTTCACAGAAGAAAGGATTTTTCAAGCCTAAGAGGGAGAAAGATGTGCTAAGTACGG[T/C]
GCTGGGTACTCCTGAGCATGGGGGTAGGGTTCGAGGTGTGTCGTCCAAGATGAGTTGGAAGGAAGGGTTCAAACATGACCCCCACTAGAAGCGTGATGCG

Reverse complement sequence

CGCATCACGCTTCTAGTGGGGGTCATGTTTGAACCCTTCCTTCCAACTCATCTTGGACGACACACCTCGAACCCTACCCCCATGCTCAGGAGTACCCAGC[A/G]
CCGTACTTAGCACATCTTTCTCCCTCTTAGGCTTGAAAAATCCTTTCTTCTGTGAACTGGATAAATTCTCTATTTTATCGGCAACACCCTGCAGCTCCGG

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 97.90% 1.50% 0.32% 0.32% NA
All Indica  2759 99.40% 0.10% 0.43% 0.04% NA
All Japonica  1512 94.70% 4.20% 0.13% 0.93% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.00% 0.60% 2.37% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 91.30% 8.00% 0.26% 0.52% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 96.30% 1.20% 0.00% 2.49% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0814660415 T -> C LOC_Os08g24290.1 missense_variant ; p.Val341Ala; MODERATE nonsynonymous_codon ; V341A Average:50.759; most accessible tissue: Minghui63 flag leaf, score: 77.828 benign -0.417 TOLERATED 1.00
vg0814660415 T -> DEL LOC_Os08g24290.1 N frameshift_variant Average:50.759; most accessible tissue: Minghui63 flag leaf, score: 77.828 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)
vg0814660415 T C 0.0 0.0 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814660415 NA 1.25E-06 mr1028 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
vg0814660415 NA 9.11E-06 mr1245 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
vg0814660415 NA 4.01E-06 mr1648 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
vg0814660415 NA 4.35E-07 mr1697 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
vg0814660415 3.83E-06 3.83E-06 mr1915 Jap_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