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Detailed information for vg0721165888:

Variant ID: vg0721165888 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21165888
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACAAACCGGTCCAACCCGTCAACCAAACCATCCCGATCCCCTTTTTGCGGCTGTACAGTTGTACGTGGGGAGGCCATATGTGTGGATCCTGTGCATAAT[C/A]
ACCCCGTTGAATCCACCCCCTTCGTTTCTCGAAAGAAATTTGAAAATATACTTTATTTTTTCATATATTGCATTTATATACCTGGCTGTGACTAATTTAC

Reverse complement sequence

GTAAATTAGTCACAGCCAGGTATATAAATGCAATATATGAAAAAATAAAGTATATTTTCAAATTTCTTTCGAGAAACGAAGGGGGTGGATTCAACGGGGT[G/T]
ATTATGCACAGGATCCACACATATGGCCTCCCCACGTACAACTGTACAGCCGCAAAAAGGGGATCGGGATGGTTTGGTTGACGGGTTGGACCGGTTTGTG

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 61.30% 24.30% 8.55% 5.86% NA
All Indica  2759 59.50% 18.80% 12.58% 9.17% NA
All Japonica  1512 59.50% 40.20% 0.26% 0.07% NA
Aus  269 74.70% 0.70% 17.10% 7.43% NA
Indica I  595 89.10% 5.20% 3.19% 2.52% NA
Indica II  465 51.80% 10.50% 23.44% 14.19% NA
Indica III  913 45.80% 33.80% 11.39% 8.98% NA
Indica Intermediate  786 57.50% 16.40% 14.63% 11.45% NA
Temperate Japonica  767 52.00% 47.30% 0.52% 0.13% NA
Tropical Japonica  504 57.90% 42.10% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 72.20% 16.70% 7.78% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0721165888 C -> DEL N N silent_mutation Average:87.442; most accessible tissue: Minghui63 root, score: 97.458 N N N N
vg0721165888 C -> A LOC_Os07g35380.1 upstream_gene_variant ; 1996.0bp to feature; MODIFIER silent_mutation Average:87.442; most accessible tissue: Minghui63 root, score: 97.458 N N N N
vg0721165888 C -> A LOC_Os07g35390.1 upstream_gene_variant ; 1333.0bp to feature; MODIFIER silent_mutation Average:87.442; most accessible tissue: Minghui63 root, score: 97.458 N N N N
vg0721165888 C -> A LOC_Os07g35380-LOC_Os07g35390 intergenic_region ; MODIFIER silent_mutation Average:87.442; most accessible tissue: Minghui63 root, score: 97.458 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)
vg0721165888 C A -0.09 -0.04 -0.02 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721165888 5.45E-07 NA mr1730 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