Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0909341432:

Variant ID: vg0909341432 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9341432
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGATGGCGTGGAGGCGACGTGCGGCAGCTTGCAGCGGTTTCCGGGCGAAACAGAGGAGCAGCCGGAGGAGAGGACGATGCAGCGACGTCGACGGAGGAGA[C/T]
GGCGACGTAGGTCGGTGCTCGGGCACAGGGGAAGGGGCTGCCGGAGGTGGTGCAGTGGCGGCAACATCACTGTTTACCCGCGAGGACGCGTCTCCGGTGG

Reverse complement sequence

CCACCGGAGACGCGTCCTCGCGGGTAAACAGTGATGTTGCCGCCACTGCACCACCTCCGGCAGCCCCTTCCCCTGTGCCCGAGCACCGACCTACGTCGCC[G/A]
TCTCCTCCGTCGACGTCGCTGCATCGTCCTCTCCTCCGGCTGCTCCTCTGTTTCGCCCGGAAACCGCTGCAAGCTGCCGCACGTCGCCTCCACGCCATCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.20% 5.50% 1.21% 2.09% NA
All Indica  2759 98.40% 0.90% 0.14% 0.54% NA
All Japonica  1512 85.30% 7.80% 2.58% 4.37% NA
Aus  269 45.70% 42.40% 5.20% 6.69% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 99.60% 0.30% 0.00% 0.11% NA
Indica Intermediate  786 95.40% 2.40% 0.51% 1.65% NA
Temperate Japonica  767 90.10% 2.90% 2.35% 4.69% NA
Tropical Japonica  504 87.30% 9.90% 0.40% 2.38% NA
Japonica Intermediate  241 65.60% 19.10% 7.88% 7.47% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0909341432 C -> DEL LOC_Os09g15310.1 N frameshift_variant Average:77.365; most accessible tissue: Zhenshan97 young leaf, score: 89.978 N N N N
vg0909341432 C -> T LOC_Os09g15310.1 synonymous_variant ; p.Asp106Asp; LOW synonymous_codon Average:77.365; most accessible tissue: Zhenshan97 young leaf, score: 89.978 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)
vg0909341432 C T -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909341432 NA 2.88E-06 mr1280 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
vg0909341432 NA 1.92E-08 mr1446 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
vg0909341432 NA 5.55E-09 mr1465 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
vg0909341432 NA 2.64E-10 mr1720 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
vg0909341432 6.13E-06 NA mr1757 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
vg0909341432 9.85E-06 6.08E-07 mr1177_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
vg0909341432 NA 6.13E-07 mr1180_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
vg0909341432 NA 5.04E-08 mr1183_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
vg0909341432 4.33E-07 NA mr1550_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
vg0909341432 NA 8.89E-14 mr1583_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
vg0909341432 NA 5.32E-07 mr1702_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
vg0909341432 NA 8.44E-08 mr1702_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
vg0909341432 NA 7.55E-07 mr1729_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
vg0909341432 NA 7.62E-08 mr1740_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
vg0909341432 5.34E-06 NA mr1757_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