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Detailed information for vg1128778120:

Variant ID: vg1128778120 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28778120
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTGTGCATGTTGGTGTGAGTGCGTGTGACTAATGTGGGTCAGGTTGTGATATTTGTGCCCAAAAACGGTTGTTTTGCCTGATTATATGTAGGTAACTT[G/A]
AGGTCAGCCTTGGTCAATGGTGAGGACCAAGACTATGCTCATGGAGGAGCAAAGGTCTAGTGTGGTCGGGATATCATGTGAAAAAGTGACTAGTCAGGAT

Reverse complement sequence

ATCCTGACTAGTCACTTTTTCACATGATATCCCGACCACACTAGACCTTTGCTCCTCCATGAGCATAGTCTTGGTCCTCACCATTGACCAAGGCTGACCT[C/T]
AAGTTACCTACATATAATCAGGCAAAACAACCGTTTTTGGGCACAAATATCACAACCTGACCCACATTAGTCACACGCACTCACACCAACATGCACACAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 14.40% 0.19% 0.00% NA
All Indica  2759 98.30% 1.60% 0.07% 0.00% NA
All Japonica  1512 60.10% 39.60% 0.40% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.50% 1.40% 0.11% 0.00% NA
Indica Intermediate  786 96.20% 3.70% 0.13% 0.00% NA
Temperate Japonica  767 77.10% 22.30% 0.65% 0.00% NA
Tropical Japonica  504 31.00% 69.00% 0.00% 0.00% NA
Japonica Intermediate  241 66.80% 32.80% 0.41% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 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
vg1128778120 G -> A LOC_Os11g47660.1 upstream_gene_variant ; 1700.0bp to feature; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1128778120 G -> A LOC_Os11g47670.1 upstream_gene_variant ; 3041.0bp to feature; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1128778120 G -> A LOC_Os11g47640.1 downstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1128778120 G -> A LOC_Os11g47650.1 downstream_gene_variant ; 133.0bp to feature; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1128778120 G -> A LOC_Os11g47650.2 downstream_gene_variant ; 133.0bp to feature; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1128778120 G -> A LOC_Os11g47650-LOC_Os11g47660 intergenic_region ; MODIFIER silent_mutation Average:67.877; most accessible tissue: Zhenshan97 panicle, score: 88.888 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)
vg1128778120 G A -0.02 -0.04 -0.03 -0.03 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128778120 9.24E-07 NA mr1261 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
vg1128778120 5.90E-07 NA mr1310 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
vg1128778120 NA 7.65E-07 mr1310 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
vg1128778120 NA 6.01E-08 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
vg1128778120 3.51E-06 NA mr1238_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
vg1128778120 5.73E-07 NA mr1310_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
vg1128778120 5.65E-06 NA mr1484_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
vg1128778120 NA 1.35E-06 mr1566_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