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Detailed information for vg1227404000:

Variant ID: vg1227404000 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27404000
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGATAAATAAGAGTAGCAACTAGTATCAATTAAGGCCGAGTTTAGTTTCAAACTTTTTCTTCAAACTTCCAGTTTTTCTATCACATCAAAACTTTTCTA[C/T]
GGCTGTGTTTAGTTCAGCGCAAAGTTTAGATTTTGGTTAAAATTGAAGATGATGTGACTGAAAAGTTGTGTGTGTATGACAGGTTGATGTGATGGAAAAG

Reverse complement sequence

CTTTTCCATCACATCAACCTGTCATACACACACAACTTTTCAGTCACATCATCTTCAATTTTAACCAAAATCTAAACTTTGCGCTGAACTAAACACAGCC[G/A]
TAGAAAAGTTTTGATGTGATAGAAAAACTGGAAGTTTGAAGAAAAAGTTTGAAACTAAACTCGGCCTTAATTGATACTAGTTGCTACTCTTATTTATCAT

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 88.20% 11.30% 0.57% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 65.70% 32.50% 1.79% 0.00% 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 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 85.40% 12.40% 2.22% 0.00% NA
Tropical Japonica  504 27.60% 71.00% 1.39% 0.00% NA
Japonica Intermediate  241 83.00% 15.80% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1227404000 C -> T LOC_Os12g44170.1 upstream_gene_variant ; 585.0bp to feature; MODIFIER silent_mutation Average:65.336; most accessible tissue: Minghui63 flag leaf, score: 85.5 N N N N
vg1227404000 C -> T LOC_Os12g44180.1 upstream_gene_variant ; 3370.0bp to feature; MODIFIER silent_mutation Average:65.336; most accessible tissue: Minghui63 flag leaf, score: 85.5 N N N N
vg1227404000 C -> T LOC_Os12g44170-LOC_Os12g44180 intergenic_region ; MODIFIER silent_mutation Average:65.336; most accessible tissue: Minghui63 flag leaf, score: 85.5 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)
vg1227404000 C T -0.01 0.0 0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227404000 NA 8.27E-10 mr1097 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
vg1227404000 NA 1.53E-12 mr1449 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
vg1227404000 NA 3.34E-08 mr1642 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
vg1227404000 NA 6.99E-11 mr1648 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
vg1227404000 NA 7.37E-07 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
vg1227404000 NA 2.05E-12 mr1097_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
vg1227404000 3.14E-06 3.85E-07 mr1648_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
vg1227404000 NA 1.44E-07 mr1765_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
vg1227404000 NA 1.11E-12 mr1781_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
vg1227404000 NA 5.97E-07 mr1781_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
vg1227404000 NA 2.50E-08 mr1786_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
vg1227404000 NA 1.00E-07 mr1807_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