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Detailed information for vg1128439104:

Variant ID: vg1128439104 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28439104
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGTTCAATTTGCATATAAATATTACATATCGTGCGTAGTGTTTCACGCAGTAAAGATTATTTATTTGAGGGTGAGTGGAAAAAAAAAGAAAAACCACCA[T/C]
GAGTACAGAATCTTCCATATGTGACGGCCTCTAATATGCCTATAATTAACGGGTCGTCACAAGAAAGTCATCTCAATCGGGCCAAAAAAAGCCCTATTGA

Reverse complement sequence

TCAATAGGGCTTTTTTTGGCCCGATTGAGATGACTTTCTTGTGACGACCCGTTAATTATAGGCATATTAGAGGCCGTCACATATGGAAGATTCTGTACTC[A/G]
TGGTGGTTTTTCTTTTTTTTTCCACTCACCCTCAAATAAATAATCTTTACTGCGTGAAACACTACGCACGATATGTAATATTTATATGCAAATTGAACGT

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 42.70% 32.70% 3.85% 20.74% NA
All Indica  2759 52.20% 23.50% 3.81% 20.48% NA
All Japonica  1512 28.80% 43.30% 4.03% 23.88% NA
Aus  269 33.50% 50.60% 3.72% 12.27% NA
Indica I  595 69.60% 25.40% 2.35% 2.69% NA
Indica II  465 19.40% 24.90% 2.37% 53.33% NA
Indica III  913 62.30% 22.30% 3.94% 11.39% NA
Indica Intermediate  786 46.80% 22.50% 5.60% 25.06% NA
Temperate Japonica  767 35.10% 36.20% 4.43% 24.25% NA
Tropical Japonica  504 23.00% 53.20% 3.37% 20.44% NA
Japonica Intermediate  241 21.20% 44.80% 4.15% 29.88% NA
VI/Aromatic  96 18.80% 66.70% 4.17% 10.42% NA
Intermediate  90 37.80% 47.80% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1128439104 T -> DEL N N silent_mutation Average:41.303; most accessible tissue: Zhenshan97 root, score: 80.448 N N N N
vg1128439104 T -> C LOC_Os11g47290.1 upstream_gene_variant ; 637.0bp to feature; MODIFIER silent_mutation Average:41.303; most accessible tissue: Zhenshan97 root, score: 80.448 N N N N
vg1128439104 T -> C LOC_Os11g47290-LOC_Os11g47300 intergenic_region ; MODIFIER silent_mutation Average:41.303; most accessible tissue: Zhenshan97 root, score: 80.448 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)
vg1128439104 T C 0.03 0.0 0.02 0.0 -0.01 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128439104 9.37E-08 NA mr1238 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
vg1128439104 NA 3.74E-06 mr1238 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
vg1128439104 1.44E-08 NA mr1309 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
vg1128439104 NA 1.32E-07 mr1309 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
vg1128439104 9.53E-08 NA mr1484 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
vg1128439104 2.16E-06 3.08E-08 mr1484 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
vg1128439104 5.56E-07 NA mr1841 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
vg1128439104 NA 3.45E-06 mr1841 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
vg1128439104 7.70E-07 NA mr1900 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
vg1128439104 NA 2.95E-06 mr1900 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
vg1128439104 6.88E-07 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
vg1128439104 NA 1.31E-06 mr1238_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
vg1128439104 7.33E-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
vg1128439104 4.36E-06 4.36E-06 mr1484_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
vg1128439104 2.06E-07 NA mr1841_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
vg1128439104 NA 1.72E-07 mr1841_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
vg1128439104 3.02E-06 NA mr1900_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
vg1128439104 NA 7.20E-06 mr1900_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