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Detailed information for vg1002292435:

Variant ID: vg1002292435 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2292435
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CCAACGAGTATGCCAGGATCAACAAAAGCAAAGACCAAGAATGGAGCAGGAGTGAAGATGAGATTGCTCCATCTGCCGGTCTCCGATGTGTAGAAGCAAG[C/T]
GAACATTTGTGTGTTGTTGCTGGCCACGCCCACCAAGGCAACATTGAAGGGGCAACAGCTGAATCCGCCGTGAACGTGGCCGTCGTCGTCGGCGGCGGCA

Reverse complement sequence

TGCCGCCGCCGACGACGACGGCCACGTTCACGGCGGATTCAGCTGTTGCCCCTTCAATGTTGCCTTGGTGGGCGTGGCCAGCAACAACACACAAATGTTC[G/A]
CTTGCTTCTACACATCGGAGACCGGCAGATGGAGCAATCTCATCTTCACTCCTGCTCCATTCTTGGTCTTTGCTTTTGTTGATCCTGGCATACTCGTTGG

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 67.10% 32.40% 0.00% 0.44% NA
All Indica  2759 60.40% 38.90% 0.00% 0.72% NA
All Japonica  1512 84.80% 15.20% 0.00% 0.00% NA
Aus  269 24.20% 75.80% 0.00% 0.00% NA
Indica I  595 69.90% 29.60% 0.00% 0.50% NA
Indica II  465 65.60% 33.50% 0.00% 0.86% NA
Indica III  913 52.00% 47.50% 0.00% 0.44% NA
Indica Intermediate  786 59.90% 38.90% 0.00% 1.15% NA
Temperate Japonica  767 91.70% 8.30% 0.00% 0.00% NA
Tropical Japonica  504 78.00% 22.00% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002292435 C -> T LOC_Os10g04770.1 missense_variant ; p.Ala112Thr; MODERATE nonsynonymous_codon ; A112T Average:76.38; most accessible tissue: Zhenshan97 panicle, score: 87.126 benign 0.381 TOLERATED 0.28
vg1002292435 C -> DEL LOC_Os10g04770.1 N frameshift_variant Average:76.38; most accessible tissue: Zhenshan97 panicle, score: 87.126 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)
vg1002292435 C T -0.01 -0.01 -0.01 -0.02 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002292435 NA 4.21E-06 mr1179 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
vg1002292435 1.11E-08 NA mr1486 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
vg1002292435 8.21E-06 1.08E-09 mr1486 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
vg1002292435 NA 4.35E-09 mr1510 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
vg1002292435 1.15E-07 NA mr1548 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
vg1002292435 NA 7.16E-08 mr1548 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
vg1002292435 9.38E-07 NA mr1588 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
vg1002292435 NA 2.02E-08 mr1588 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
vg1002292435 2.32E-06 3.62E-13 mr1624 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
vg1002292435 NA 7.25E-08 mr1624 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
vg1002292435 6.23E-07 NA mr1486_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
vg1002292435 NA 3.57E-08 mr1486_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
vg1002292435 NA 5.74E-06 mr1588_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
vg1002292435 NA 6.02E-10 mr1624_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
vg1002292435 NA 3.79E-07 mr1721_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