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Detailed information for vg1127985849:

Variant ID: vg1127985849 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27985849
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.09, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTGACGGAGGGTCACAACCATGACAACCGGAGGAAGGACTGGATGAAGCAGATCCGAGACGTCGCCTATGACGTTGAGGACTGCATCGATGACTTTGC[G/C]
CACCGGCTCCCCCAGGATTCAATCAGCGATGCCAAATGCTCCTTCATACTCACAAAAATGTATGAACTCTTGACATGGTGGCCTCGTCGCGATATTGCTT

Reverse complement sequence

AAGCAATATCGCGACGAGGCCACCATGTCAAGAGTTCATACATTTTTGTGAGTATGAAGGAGCATTTGGCATCGCTGATTGAATCCTGGGGGAGCCGGTG[C/G]
GCAAAGTCATCGATGCAGTCCTCAACGTCATAGGCGACGTCTCGGATCTGCTTCATCCAGTCCTTCCTCCGGTTGTCATGGTTGTGACCCTCCGTCACAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.30% 43.50% 2.50% 3.68% NA
All Indica  2759 57.30% 38.30% 1.63% 2.75% NA
All Japonica  1512 39.90% 49.30% 4.56% 6.22% NA
Aus  269 32.70% 67.30% 0.00% 0.00% NA
Indica I  595 77.30% 20.80% 1.18% 0.67% NA
Indica II  465 49.90% 45.20% 1.94% 3.01% NA
Indica III  913 54.70% 38.70% 1.64% 5.04% NA
Indica Intermediate  786 49.60% 47.10% 1.78% 1.53% NA
Temperate Japonica  767 49.90% 44.20% 3.52% 2.35% NA
Tropical Japonica  504 25.00% 56.90% 5.75% 12.30% NA
Japonica Intermediate  241 39.40% 49.40% 5.39% 5.81% NA
VI/Aromatic  96 65.60% 29.20% 2.08% 3.12% NA
Intermediate  90 44.40% 52.20% 2.22% 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
vg1127985849 G -> DEL LOC_Os11g46210.1 N frameshift_variant Average:75.34; most accessible tissue: Zhenshan97 root, score: 90.979 N N N N
vg1127985849 G -> C LOC_Os11g46210.1 synonymous_variant ; p.Ala89Ala; LOW synonymous_codon Average:75.34; most accessible tissue: Zhenshan97 root, score: 90.979 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)
vg1127985849 G C 0.0 0.0 0.0 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127985849 3.60E-07 3.60E-07 mr1649 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