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Detailed information for vg0316331996:

Variant ID: vg0316331996 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16331996
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGCTAACGCCGCCCTCCCAACCGGTACCAAGCCCTTCTCCTTCCAGTCGCTCGCCGCCCACATCTTGTGTGCTGTCTCCCGCGCCCGCGACCTCGGCC[C/T]
CTCTGACATCACCGTCTTCCTAATTGTTGCGTCCCCTCTCGACTGCCCGCCGTGCGCCGCCGCCCACCACCCACCCTAGCGCGTCGCCGTGCGCGCCGAC

Reverse complement sequence

GTCGGCGCGCACGGCGACGCGCTAGGGTGGGTGGTGGGCGGCGGCGCACGGCGGGCAGTCGAGAGGGGACGCAACAATTAGGAAGACGGTGATGTCAGAG[G/A]
GGCCGAGGTCGCGGGCGCGGGAGACAGCACACAAGATGTGGGCGGCGAGCGACTGGAAGGAGAAGGGCTTGGTACCGGTTGGGAGGGCGGCGTTAGCGCG

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 94.20% 5.80% 0.02% 0.00% NA
All Indica  2759 95.50% 4.50% 0.04% 0.00% NA
All Japonica  1512 91.10% 8.90% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 92.00% 8.00% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 86.30% 13.70% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0316331996 C -> T LOC_Os03g28350.1 missense_variant ; p.Pro241Leu; MODERATE nonsynonymous_codon ; P241L Average:76.27; most accessible tissue: Zhenshan97 young leaf, score: 88.513 unknown unknown DELETERIOUS 0.00

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)
vg0316331996 C T -0.01 -0.02 -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
vg0316331996 2.09E-06 NA Grain_length 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
vg0316331996 8.67E-06 NA Grain_length Jap_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
vg0316331996 2.08E-06 NA mr1836_2 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
vg0316331996 NA 6.11E-08 mr1836_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