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Detailed information for vg1214989214:

Variant ID: vg1214989214 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14989214
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, C: 0.26, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TTATCAACTAGACTGTTGTAGCGACATTTCGCCTTCTATCAATTTAAATTTACTTGTGGACCATTGAACTCCATATATTGTTGTCAAAGACTCTACGTCT[C/A]
TATGGTCTTACACCGGGATCGACCAAGTGAGTACAGCAAATATTGATAAGGGGAGTCGTGGATAACATAAGATGCTTTCGTGAATACTGTTTGTTTCCGT

Reverse complement sequence

ACGGAAACAAACAGTATTCACGAAAGCATCTTATGTTATCCACGACTCCCCTTATCAATATTTGCTGTACTCACTTGGTCGATCCCGGTGTAAGACCATA[G/T]
AGACGTAGAGTCTTTGACAACAATATATGGAGTTCAATGGTCCACAAGTAAATTTAAATTGATAGAAGGCGAAATGTCGCTACAACAGTCTAGTTGATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.40% 34.30% 0.28% 0.02% NA
All Indica  2759 52.70% 47.00% 0.25% 0.00% NA
All Japonica  1512 80.80% 19.10% 0.13% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 44.00% 56.00% 0.00% 0.00% NA
Indica II  465 49.70% 50.10% 0.22% 0.00% NA
Indica III  913 61.60% 38.00% 0.44% 0.00% NA
Indica Intermediate  786 50.80% 49.00% 0.25% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 68.50% 31.30% 0.20% 0.00% NA
Japonica Intermediate  241 74.30% 25.30% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 66.70% 27.80% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214989214 C -> DEL N N silent_mutation Average:70.229; most accessible tissue: Zhenshan97 root, score: 94.079 N N N N
vg1214989214 C -> A LOC_Os12g25830.1 upstream_gene_variant ; 3363.0bp to feature; MODIFIER silent_mutation Average:70.229; most accessible tissue: Zhenshan97 root, score: 94.079 N N N N
vg1214989214 C -> A LOC_Os12g25840.1 intron_variant ; MODIFIER silent_mutation Average:70.229; most accessible tissue: Zhenshan97 root, score: 94.079 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)
vg1214989214 C A 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214989214 NA 2.59E-06 mr1002_2 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
vg1214989214 NA 7.86E-06 mr1228_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
vg1214989214 NA 2.71E-06 mr1232_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
vg1214989214 NA 1.88E-07 mr1376_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
vg1214989214 NA 5.79E-09 mr1422_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
vg1214989214 NA 1.06E-07 mr1431_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
vg1214989214 NA 7.15E-06 mr1557_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
vg1214989214 NA 2.67E-06 mr1583_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
vg1214989214 NA 6.26E-07 mr1606_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
vg1214989214 NA 1.39E-07 mr1696_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
vg1214989214 NA 6.88E-06 mr1830_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
vg1214989214 2.52E-06 2.52E-06 mr1869_2 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
vg1214989214 NA 5.50E-06 mr1873_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
vg1214989214 NA 4.47E-06 mr1884_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
vg1214989214 NA 2.61E-07 mr1905_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
vg1214989214 NA 1.98E-10 mr1916_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
vg1214989214 NA 8.50E-07 mr1944_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