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Detailed information for vg1222498818:

Variant ID: vg1222498818 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 22498818
Reference Allele: TAlternative Allele: A,TGA
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, T: 0.19, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTAAGTACCTGAATTAGTTCACCGTAATAGTAATTCGAGCGCTGCTTGATTTGGATAGTCCTTAAGTGCCTCTTCAATAACAGCCGTGTTCTCACCCA[T/A,TGA]
GTAATCAATGGTTACATGCCGAAGGGAGTGGAGGTTCTCCAAACCTAAATCATTTAAGTCACCCCTCCTTAGTCTGGTCCCAATACGAAGACAAAGCCTT

Reverse complement sequence

AAGGCTTTGTCTTCGTATTGGGACCAGACTAAGGAGGGGTGACTTAAATGATTTAGGTTTGGAGAACCTCCACTCCCTTCGGCATGTAACCATTGATTAC[A/T,TCA]
TGGGTGAGAACACGGCTGTTATTGAAGAGGCACTTAAGGACTATCCAAATCAAGCAGCGCTCGAATTACTATTACGGTGAACTAATTCAGGTACTTAGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.50% 33.60% 4.40% 12.42% TGA: 0.06%
All Indica  2759 22.30% 56.30% 5.65% 15.59% TGA: 0.11%
All Japonica  1512 91.30% 1.50% 2.58% 4.56% NA
Aus  269 69.90% 0.00% 4.09% 26.02% NA
Indica I  595 41.20% 40.00% 3.53% 15.29% NA
Indica II  465 11.60% 60.00% 1.29% 27.10% NA
Indica III  913 17.10% 62.50% 9.09% 10.95% TGA: 0.33%
Indica Intermediate  786 20.50% 59.30% 5.85% 14.38% NA
Temperate Japonica  767 94.10% 1.70% 3.00% 1.17% NA
Tropical Japonica  504 95.20% 1.40% 0.79% 2.58% NA
Japonica Intermediate  241 74.30% 1.20% 4.98% 19.50% NA
VI/Aromatic  96 87.50% 2.10% 2.08% 8.33% NA
Intermediate  90 78.90% 10.00% 0.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1222498818 T -> DEL LOC_Os12g36730.1 N frameshift_variant Average:75.551; most accessible tissue: Minghui63 root, score: 85.968 N N N N
vg1222498818 T -> A LOC_Os12g36730.1 missense_variant ; p.Met709Leu; MODERATE nonsynonymous_codon ; M709S Average:75.551; most accessible tissue: Minghui63 root, score: 85.968 unknown unknown TOLERATED 0.46
vg1222498818 T -> A LOC_Os12g36730.1 missense_variant ; p.Met709Leu; MODERATE nonsynonymous_codon ; M709W Average:75.551; most accessible tissue: Minghui63 root, score: 85.968 unknown unknown TOLERATED 0.18
vg1222498818 T -> A LOC_Os12g36730.1 missense_variant ; p.Met709Leu; MODERATE nonsynonymous_codon ; M709L Average:75.551; most accessible tissue: Minghui63 root, score: 85.968 unknown unknown TOLERATED 0.67
vg1222498818 T -> TGA LOC_Os12g36730.1 frameshift_variant ; p.Met709fs; HIGH frameshift_variant Average:75.551; most accessible tissue: Minghui63 root, score: 85.968 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)
vg1222498818 T A -0.06 -0.02 -0.02 -0.04 -0.04 -0.05
vg1222498818 T TGA -0.08 -0.11 -0.1 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222498818 NA 4.93E-07 mr1279 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