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Detailed information for vg1127224190:

Variant ID: vg1127224190 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27224190
Reference Allele: GAlternative Allele: C,T
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATGTTGAGAAGATCTTTGAGAAGCTAGAACCTCCACACAACTTAGAAGATCTTGTTATCGGGGATTTCTTTGGGCGAAGGTTCCCCACCTGGCTTGGTA[G/C,T]
TACCCATTTGTCTTCAGTGAAATACGTGCTCCTCATAGATTGCAAATCTTGTGTGCATCTTCCCCCAATCGGACAGCTACCAAACTTGAAATACCTAAAA

Reverse complement sequence

TTTTAGGTATTTCAAGTTTGGTAGCTGTCCGATTGGGGGAAGATGCACACAAGATTTGCAATCTATGAGGAGCACGTATTTCACTGAAGACAAATGGGTA[C/G,A]
TACCAAGCCAGGTGGGGAACCTTCGCCCAAAGAAATCCCCGATAACAAGATCTTCTAAGTTGTGTGGAGGTTCTAGCTTCTCAAAGATCTTCTCAACATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.40% 0.80% 4.76% 21.03% T: 0.04%
All Indica  2759 85.60% 0.10% 3.41% 10.80% NA
All Japonica  1512 56.00% 2.10% 7.87% 33.99% NA
Aus  269 37.20% 0.00% 1.86% 60.97% NA
Indica I  595 84.00% 0.30% 4.20% 11.43% NA
Indica II  465 93.80% 0.00% 0.43% 5.81% NA
Indica III  913 85.00% 0.00% 4.16% 10.84% NA
Indica Intermediate  786 82.80% 0.30% 3.69% 13.23% NA
Temperate Japonica  767 58.30% 1.30% 10.43% 29.99% NA
Tropical Japonica  504 51.80% 0.40% 6.35% 41.47% NA
Japonica Intermediate  241 57.70% 8.30% 2.90% 31.12% NA
VI/Aromatic  96 90.60% 1.00% 4.17% 4.17% NA
Intermediate  90 78.90% 0.00% 3.33% 15.56% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127224190 G -> T LOC_Os11g44960.1 missense_variant ; p.Ser779Ile; MODERATE nonsynonymous_codon ; S779I Average:53.525; most accessible tissue: Minghui63 flag leaf, score: 95.901 benign 1.372 DELETERIOUS 0.03
vg1127224190 G -> DEL LOC_Os11g44960.1 N frameshift_variant Average:53.525; most accessible tissue: Minghui63 flag leaf, score: 95.901 N N N N
vg1127224190 G -> C LOC_Os11g44960.1 missense_variant ; p.Ser779Thr; MODERATE nonsynonymous_codon ; S779T Average:53.525; most accessible tissue: Minghui63 flag leaf, score: 95.901 benign -0.466 TOLERATED 1.00

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)
vg1127224190 G C -0.02 0.0 0.0 0.0 -0.01 -0.02
vg1127224190 G T -0.1 -0.05 -0.06 -0.08 -0.09 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127224190 1.95E-08 5.82E-09 mr1350_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