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Detailed information for vg0907993257:

Variant ID: vg0907993257 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7993257
Reference Allele: TAlternative Allele: C,G
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGAGTACGTGTACTTCTTCCCTTCTATAAATACCAAATCTAATACAAAATATGATACATTTTTCTGTTCATATTTATAATACTATCATATTTTATGAGA[T/C,G]
GAAGGAAATAGGTCATCGGGAGTCGTGCTGGCAAGGGTGGGGCCCAGCTGAGGGACGAGACCGGGGGAGGAGAGGGGGACAGGCAGGTGGGTCCCGACCC

Reverse complement sequence

GGGTCGGGACCCACCTGCCTGTCCCCCTCTCCTCCCCCGGTCTCGTCCCTCAGCTGGGCCCCACCCTTGCCAGCACGACTCCCGATGACCTATTTCCTTC[A/G,C]
TCTCATAAAATATGATAGTATTATAAATATGAACAGAAAAATGTATCATATTTTGTATTAGATTTGGTATTTATAGAAGGGAAGAAGTACACGTACTCGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.00% 13.60% 0.38% 0.00% G: 0.02%
All Indica  2759 97.60% 2.40% 0.04% 0.00% NA
All Japonica  1512 75.10% 24.80% 0.07% 0.00% NA
Aus  269 56.90% 37.20% 5.58% 0.00% G: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.30% 0.13% 0.00% NA
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 41.30% 58.70% 0.00% 0.00% NA
Japonica Intermediate  241 85.10% 14.50% 0.41% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 74.40% 24.40% 1.11% 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
vg0907993257 T -> G LOC_Os09g13670.1 upstream_gene_variant ; 2139.0bp to feature; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 N N N N
vg0907993257 T -> G LOC_Os09g13680.1 upstream_gene_variant ; 2481.0bp to feature; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 N N N N
vg0907993257 T -> G LOC_Os09g13670-LOC_Os09g13680 intergenic_region ; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 N N N N
vg0907993257 T -> C LOC_Os09g13670.1 upstream_gene_variant ; 2139.0bp to feature; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 N N N N
vg0907993257 T -> C LOC_Os09g13680.1 upstream_gene_variant ; 2481.0bp to feature; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 N N N N
vg0907993257 T -> C LOC_Os09g13670-LOC_Os09g13680 intergenic_region ; MODIFIER silent_mutation Average:86.004; most accessible tissue: Minghui63 panicle, score: 99.575 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)
vg0907993257 T C 0.01 0.05 0.02 0.01 0.01 0.01
vg0907993257 T G 0.03 0.05 0.02 0.02 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907993257 NA 5.33E-06 mr1002 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
vg0907993257 NA 1.03E-06 mr1401 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
vg0907993257 NA 1.36E-08 mr1423 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
vg0907993257 NA 7.52E-12 mr1559 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
vg0907993257 NA 3.18E-06 mr1236_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
vg0907993257 NA 7.83E-06 mr1379_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
vg0907993257 NA 2.07E-07 mr1559_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