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Detailed information for vg0400063937:

Variant ID: vg0400063937 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 63937
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTGGCCTTCGCCGCCGCCGACTGCTGTCCTCGCCTATACGGTTAGTTGGTTACACCACAATTCACGGGCGTCCACGTCTTCACCGACCGGCTGGCCTTC[G/A]
CCGCCGCCGACTGGTGTTTCCGCCTGCATTGCTGGCCTATTATGCCGCCGCTGTTGGGCATCTACGACTTCACCGACCGGCTGGCCTTCGCCGCCGCCGA

Reverse complement sequence

TCGGCGGCGGCGAAGGCCAGCCGGTCGGTGAAGTCGTAGATGCCCAACAGCGGCGGCATAATAGGCCAGCAATGCAGGCGGAAACACCAGTCGGCGGCGG[C/T]
GAAGGCCAGCCGGTCGGTGAAGACGTGGACGCCCGTGAATTGTGGTGTAACCAACTAACCGTATAGGCGAGGACAGCAGTCGGCGGCGGCGAAGGCCAGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.40% 0.70% 1.10% 15.81% NA
All Indica  2759 87.70% 0.40% 0.72% 11.24% NA
All Japonica  1512 69.30% 1.20% 1.98% 27.51% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 85.90% 0.30% 1.18% 12.61% NA
Indica II  465 94.60% 0.00% 0.43% 4.95% NA
Indica III  913 89.60% 0.50% 0.77% 9.09% NA
Indica Intermediate  786 82.70% 0.40% 0.51% 16.41% NA
Temperate Japonica  767 91.30% 0.50% 0.13% 8.08% NA
Tropical Japonica  504 47.00% 1.60% 4.56% 46.83% NA
Japonica Intermediate  241 46.10% 2.50% 2.49% 48.96% NA
VI/Aromatic  96 90.60% 3.10% 1.04% 5.21% NA
Intermediate  90 80.00% 1.10% 1.11% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0400063937 G -> DEL LOC_Os04g01080.1 N frameshift_variant Average:64.287; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0400063937 G -> A LOC_Os04g01080.1 missense_variant ; p.Ala24Thr; MODERATE nonsynonymous_codon ; A24T Average:64.287; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 benign 0.577 TOLERATED 0.22

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)
vg0400063937 G A 0.0 0.01 0.0 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400063937 NA 9.31E-06 mr1189 Ind_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
vg0400063937 NA 1.49E-06 mr1252 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
vg0400063937 NA 7.32E-09 mr1354 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
vg0400063937 NA 7.19E-08 mr1388 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
vg0400063937 NA 6.27E-07 mr1458 Ind_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
vg0400063937 NA 2.05E-07 mr1554 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
vg0400063937 NA 3.74E-06 mr1594 Ind_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
vg0400063937 NA 1.55E-08 mr1602 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
vg0400063937 2.88E-06 NA mr1698 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
vg0400063937 NA 3.85E-06 mr1725 Ind_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
vg0400063937 NA 1.38E-06 mr1756 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
vg0400063937 NA 1.15E-07 mr1798 Ind_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
vg0400063937 NA 2.50E-06 mr1990 Ind_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
vg0400063937 NA 4.49E-06 mr1252_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
vg0400063937 NA 4.27E-06 mr1263_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
vg0400063937 NA 3.67E-11 mr1769_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
vg0400063937 NA 1.98E-07 mr1798_2 Ind_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