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Detailed information for vg1226956034:

Variant ID: vg1226956034 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 26956034
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGCCGCCCACGGGCCACAGCCATCTAGCCCTCTAAGCCCCGAGGAAGCCACCTCCCTCCTCCTCTTCCCACTCCCCTAACCCCTTTCCTACCCTGACCC[C/T]
AACCTCAAACCCTACCAAAGTTGGGGATGTCGCCGGCGCCGACAAGAAGGGGAGCCCGCCGGAGTTGAAGGAGAGAAGCCGATGCATGAATCTTGGCATA

Reverse complement sequence

TATGCCAAGATTCATGCATCGGCTTCTCTCCTTCAACTCCGGCGGGCTCCCCTTCTTGTCGGCGCCGGCGACATCCCCAACTTTGGTAGGGTTTGAGGTT[G/A]
GGGTCAGGGTAGGAAAGGGGTTAGGGGAGTGGGAAGAGGAGGAGGGAGGTGGCTTCCTCGGGGCTTAGAGGGCTAGATGGCTGTGGCCCGTGGGCGGCGG

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 47.20% 12.80% 0.15% 39.82% NA
All Indica  2759 78.00% 3.40% 0.07% 18.56% NA
All Japonica  1512 1.70% 14.60% 0.20% 83.47% NA
Aus  269 3.30% 94.80% 0.37% 1.49% NA
Indica I  595 37.50% 7.40% 0.17% 54.96% NA
Indica II  465 94.20% 1.10% 0.00% 4.73% NA
Indica III  913 91.80% 1.20% 0.11% 6.90% NA
Indica Intermediate  786 83.10% 4.20% 0.00% 12.72% NA
Temperate Japonica  767 1.30% 25.90% 0.26% 72.49% NA
Tropical Japonica  504 2.00% 2.00% 0.20% 95.83% NA
Japonica Intermediate  241 2.50% 5.00% 0.00% 92.53% NA
VI/Aromatic  96 3.10% 19.80% 1.04% 76.04% NA
Intermediate  90 46.70% 18.90% 0.00% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1226956034 C -> DEL N N silent_mutation Average:52.644; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg1226956034 C -> T LOC_Os12g43450.1 upstream_gene_variant ; 4453.0bp to feature; MODIFIER silent_mutation Average:52.644; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg1226956034 C -> T LOC_Os12g43440.1 downstream_gene_variant ; 108.0bp to feature; MODIFIER silent_mutation Average:52.644; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg1226956034 C -> T LOC_Os12g43410-LOC_Os12g43440 intergenic_region ; MODIFIER silent_mutation Average:52.644; most accessible tissue: Minghui63 panicle, score: 88.281 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)
vg1226956034 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
vg1226956034 NA 2.60E-06 mr1126 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
vg1226956034 NA 3.12E-14 mr1166 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
vg1226956034 NA 4.86E-27 mr1210 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
vg1226956034 NA 5.64E-14 mr1270 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
vg1226956034 NA 1.60E-31 mr1305 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
vg1226956034 NA 1.05E-06 mr1321 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
vg1226956034 NA 5.37E-06 mr1349 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
vg1226956034 NA 3.73E-08 mr1403 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
vg1226956034 NA 1.56E-16 mr1409 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
vg1226956034 NA 1.99E-08 mr1585 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
vg1226956034 9.09E-06 6.42E-34 mr1586 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
vg1226956034 NA 2.22E-15 mr1649 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
vg1226956034 NA 8.29E-07 mr1762 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
vg1226956034 NA 4.77E-18 mr1765 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
vg1226956034 7.08E-06 NA mr1128_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
vg1226956034 4.25E-06 NA mr1152_2 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
vg1226956034 5.58E-06 NA mr1154_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
vg1226956034 NA 1.56E-06 mr1344_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
vg1226956034 NA 1.89E-13 mr1409_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
vg1226956034 NA 1.93E-08 mr1510_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
vg1226956034 NA 6.44E-06 mr1511_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
vg1226956034 NA 2.05E-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
vg1226956034 NA 7.00E-10 mr1649_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
vg1226956034 NA 5.46E-06 mr1672_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
vg1226956034 NA 4.33E-08 mr1707_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
vg1226956034 NA 2.85E-06 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
vg1226956034 NA 7.34E-09 mr1860_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