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Detailed information for vg1127488862:

Variant ID: vg1127488862 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27488862
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTATGCATTCCATTCCATTCCATTTCATTTTATTTCCCCAACCACTTTTGAGATTTGCTAGCAGCATAGTGTGGTGCCACCCCCTCCCTCTTGTTTGTT[G/C]
GAGTAGTTTTTTTTTTCGCAGTAGTCCTTTTCTTTTCGCAATTGGTTGTTGCAGTGATTTTTTTTTTACTCTCTTCCAGCATACGTATGTCTAGCCGATT

Reverse complement sequence

AATCGGCTAGACATACGTATGCTGGAAGAGAGTAAAAAAAAAATCACTGCAACAACCAATTGCGAAAAGAAAAGGACTACTGCGAAAAAAAAAACTACTC[C/G]
AACAAACAAGAGGGAGGGGGTGGCACCACACTATGCTGCTAGCAAATCTCAAAAGTGGTTGGGGAAATAAAATGAAATGGAATGGAATGGAATGCATACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.90% 0.20% 7.11% 26.79% NA
All Indica  2759 55.50% 0.30% 9.79% 34.43% NA
All Japonica  1512 81.50% 0.10% 2.84% 15.61% NA
Aus  269 95.90% 0.00% 1.49% 2.60% NA
Indica I  595 56.50% 0.80% 9.41% 33.28% NA
Indica II  465 26.50% 0.00% 13.98% 59.57% NA
Indica III  913 68.20% 0.20% 8.00% 23.55% NA
Indica Intermediate  786 57.00% 0.30% 9.67% 33.08% NA
Temperate Japonica  767 87.70% 0.10% 1.56% 10.56% NA
Tropical Japonica  504 70.20% 0.00% 5.36% 24.40% NA
Japonica Intermediate  241 85.10% 0.00% 1.66% 13.28% NA
VI/Aromatic  96 32.30% 0.00% 13.54% 54.17% NA
Intermediate  90 70.00% 0.00% 6.67% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127488862 G -> DEL N N silent_mutation Average:54.164; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg1127488862 G -> C LOC_Os11g45410.1 downstream_gene_variant ; 3617.0bp to feature; MODIFIER silent_mutation Average:54.164; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg1127488862 G -> C LOC_Os11g45400.1 intron_variant ; MODIFIER silent_mutation Average:54.164; most accessible tissue: Zhenshan97 panicle, score: 80.486 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)
vg1127488862 G C 0.0 -0.01 -0.02 -0.02 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127488862 NA 1.28E-06 mr1124 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
vg1127488862 NA 3.42E-06 mr1285 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
vg1127488862 NA 6.58E-10 mr1299 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
vg1127488862 2.64E-06 2.64E-06 mr1299 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
vg1127488862 NA 2.41E-06 mr1448 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
vg1127488862 NA 9.06E-11 mr1666 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
vg1127488862 NA 6.74E-06 mr1704 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
vg1127488862 NA 1.21E-06 mr1756 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
vg1127488862 NA 3.26E-06 mr1872 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
vg1127488862 NA 9.01E-06 mr1876 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
vg1127488862 NA 7.12E-06 mr1976 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