Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0907278736:

Variant ID: vg0907278736 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7278736
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.33, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGGGCAGCACGGATGGATGACCTTCTGTTGAAACGAGATGTCGCGATGTTGTCATCAAGGATGCGGAGGATTGGGTCAGACTGGTTGTTCTGCAGCAA[T/C]
GGTGGCACCTTCAAGTCACGCGGCAGCTGAGACCACTGTGCACGGCAGATGGGACATGTAACATTGCCGTGCCGAATGTTGGAGGCGATGCATAGGAAGT

Reverse complement sequence

ACTTCCTATGCATCGCCTCCAACATTCGGCACGGCAATGTTACATGTCCCATCTGCCGTGCACAGTGGTCTCAGCTGCCGCGTGACTTGAAGGTGCCACC[A/G]
TTGCTGCAGAACAACCAGTCTGACCCAATCCTCCGCATCCTTGATGACAACATCGCGACATCTCGTTTCAACAGAAGGTCATCCATCCGTGCTGCCCGGT

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 61.80% 38.10% 0.06% 0.00% NA
All Indica  2759 90.50% 9.40% 0.07% 0.00% NA
All Japonica  1512 7.40% 92.60% 0.00% 0.00% NA
Aus  269 90.30% 9.30% 0.37% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 81.90% 18.00% 0.11% 0.00% NA
Indica Intermediate  786 90.60% 9.30% 0.13% 0.00% NA
Temperate Japonica  767 11.70% 88.30% 0.00% 0.00% NA
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 41.10% 58.90% 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
vg0907278736 T -> C LOC_Os09g12720.1 synonymous_variant ; p.Pro148Pro; LOW synonymous_codon Average:84.649; most accessible tissue: Zhenshan97 panicle, score: 95.323 N N N N
vg0907278736 T -> C LOC_Os09g12720.2 synonymous_variant ; p.Pro72Pro; LOW synonymous_codon Average:84.649; most accessible tissue: Zhenshan97 panicle, score: 95.323 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)
vg0907278736 T C 0.0 -0.01 0.0 0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907278736 NA 1.75E-10 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0907278736 NA 1.26E-13 mr1924 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
vg0907278736 NA 6.64E-07 mr1060_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
vg0907278736 NA 3.92E-06 mr1354_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
vg0907278736 NA 2.63E-08 mr1549_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
vg0907278736 7.34E-07 7.34E-07 mr1568_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
vg0907278736 NA 4.74E-14 mr1579_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
vg0907278736 NA 5.02E-15 mr1686_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
vg0907278736 NA 2.13E-33 mr1723_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
vg0907278736 NA 1.06E-08 mr1757_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
vg0907278736 NA 9.70E-07 mr1902_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