Search for Variation information by Variation ID:

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

Detailed information for vg0724490397:

Variant ID: vg0724490397 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24490397
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCAAAGTTTAAATCTTAAAGTCAAAATTTTATAAAACTAATTTGAAAGTTTTCAATCGGTTAGTAAAAATAATCTTCCAGAAAAAAATATTATCTTAA[C/T]
TATTGTCGTTATATAAAACTAATTTAGTTAGTTAGGCTAAACTACTCCCGAGGTGGTGCGCGCCGGGTAGCTAAATGGGTGCCACCTATTTACTCACCAA

Reverse complement sequence

TTGGTGAGTAAATAGGTGGCACCCATTTAGCTACCCGGCGCGCACCACCTCGGGAGTAGTTTAGCCTAACTAACTAAATTAGTTTTATATAACGACAATA[G/A]
TTAAGATAATATTTTTTTCTGGAAGATTATTTTTACTAACCGATTGAAAACTTTCAAATTAGTTTTATAAAATTTTGACTTTAAGATTTAAACTTTGAAG

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 69.30% 26.80% 0.63% 3.24% NA
All Indica  2759 96.60% 3.10% 0.04% 0.25% NA
All Japonica  1512 33.70% 55.50% 1.46% 9.33% NA
Aus  269 16.70% 81.00% 1.86% 0.37% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 90.30% 8.20% 0.22% 1.29% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.60% 0.00% 0.13% NA
Temperate Japonica  767 60.80% 37.90% 0.13% 1.17% NA
Tropical Japonica  504 1.40% 76.00% 2.78% 19.84% NA
Japonica Intermediate  241 15.40% 68.50% 2.90% 13.28% NA
VI/Aromatic  96 5.20% 92.70% 2.08% 0.00% NA
Intermediate  90 55.60% 40.00% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0724490397 C -> DEL N N silent_mutation Average:92.187; most accessible tissue: Minghui63 panicle, score: 97.406 N N N N
vg0724490397 C -> T LOC_Os07g40910.1 upstream_gene_variant ; 1948.0bp to feature; MODIFIER silent_mutation Average:92.187; most accessible tissue: Minghui63 panicle, score: 97.406 N N N N
vg0724490397 C -> T LOC_Os07g40920.1 upstream_gene_variant ; 579.0bp to feature; MODIFIER silent_mutation Average:92.187; most accessible tissue: Minghui63 panicle, score: 97.406 N N N N
vg0724490397 C -> T LOC_Os07g40930.1 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:92.187; most accessible tissue: Minghui63 panicle, score: 97.406 N N N N
vg0724490397 C -> T LOC_Os07g40910-LOC_Os07g40920 intergenic_region ; MODIFIER silent_mutation Average:92.187; most accessible tissue: Minghui63 panicle, score: 97.406 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)
vg0724490397 C T 0.02 0.05 0.06 0.01 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724490397 NA 1.14E-09 mr1047 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
vg0724490397 6.50E-07 NA mr1343 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
vg0724490397 4.02E-16 NA 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
vg0724490397 2.05E-15 1.09E-08 mr1354 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
vg0724490397 NA 7.82E-18 mr1552 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
vg0724490397 NA 6.10E-10 mr1648 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
vg0724490397 8.08E-10 NA mr1829 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
vg0724490397 3.65E-12 NA mr1829 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
vg0724490397 4.70E-06 NA mr1902 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
vg0724490397 6.37E-08 NA mr1902 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
vg0724490397 NA 1.02E-13 mr1047_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
vg0724490397 6.21E-06 NA mr1138_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
vg0724490397 NA 1.74E-16 mr1189_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
vg0724490397 2.39E-26 NA mr1354_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
vg0724490397 5.09E-27 9.03E-09 mr1354_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
vg0724490397 NA 1.41E-14 mr1552_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
vg0724490397 1.66E-06 NA mr1567_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
vg0724490397 2.05E-06 NA mr1567_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
vg0724490397 NA 3.44E-08 mr1642_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
vg0724490397 7.27E-07 NA mr1679_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
vg0724490397 1.67E-06 NA mr1679_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
vg0724490397 NA 3.17E-10 mr1782_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
vg0724490397 1.09E-16 NA mr1829_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
vg0724490397 6.08E-16 5.73E-08 mr1829_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
vg0724490397 2.12E-15 NA mr1902_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
vg0724490397 1.51E-14 3.18E-06 mr1902_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