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Detailed information for vg0805947641:

Variant ID: vg0805947641 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5947641
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAATTCAAAGATAGACAGGCTATCTCACATCTGATTCAGTTATGTTCCATTACAGATTCTTCTTCCAAAGAGACTGTACCTTCTGAAGTTCAGCAACTG[T/C]
TGTCTCAATTTGCACAAGTTTTTGAGGAGCCTGATGGATTACCCCCTTCAGAGTATTTGATCACTCAATTCCTCTGATTCCTGGGGCAATGCCAGTAAAT

Reverse complement sequence

ATTTACTGGCATTGCCCCAGGAATCAGAGGAATTGAGTGATCAAATACTCTGAAGGGGGTAATCCATCAGGCTCCTCAAAAACTTGTGCAAATTGAGACA[A/G]
CAGTTGCTGAACTTCAGAAGGTACAGTCTCTTTGGAAGAAGAATCTGTAATGGAACATAACTGAATCAGATGTGAGATAGCCTGTCTATCTTTGAATTCC

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 41.50% 27.00% 4.99% 26.51% NA
All Indica  2759 54.30% 8.10% 7.25% 30.37% NA
All Japonica  1512 21.00% 68.00% 0.73% 10.32% NA
Aus  269 38.70% 0.70% 4.09% 56.51% NA
Indica I  595 25.70% 3.70% 18.32% 52.27% NA
Indica II  465 85.60% 2.80% 2.15% 9.46% NA
Indica III  913 58.80% 11.10% 2.74% 27.38% NA
Indica Intermediate  786 52.00% 11.20% 7.12% 29.64% NA
Temperate Japonica  767 4.30% 83.80% 1.04% 10.82% NA
Tropical Japonica  504 49.00% 42.50% 0.20% 8.33% NA
Japonica Intermediate  241 15.40% 71.00% 0.83% 12.86% NA
VI/Aromatic  96 15.60% 2.10% 4.17% 78.12% NA
Intermediate  90 32.20% 21.10% 11.11% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805947641 T -> C LOC_Os08g10244.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:41.991; most accessible tissue: Minghui63 young leaf, score: 87.965 N N N N
vg0805947641 T -> C LOC_Os08g10244.1 5_prime_UTR_variant ; 89.0bp to feature; MODIFIER silent_mutation Average:41.991; most accessible tissue: Minghui63 young leaf, score: 87.965 N N N N
vg0805947641 T -> C LOC_Os08g10250.1 upstream_gene_variant ; 3523.0bp to feature; MODIFIER silent_mutation Average:41.991; most accessible tissue: Minghui63 young leaf, score: 87.965 N N N N
vg0805947641 T -> C LOC_Os08g10250 intragenic_variant ; MODIFIER silent_mutation Average:41.991; most accessible tissue: Minghui63 young leaf, score: 87.965 N N N N
vg0805947641 T -> DEL N N silent_mutation Average:41.991; most accessible tissue: Minghui63 young leaf, score: 87.965 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)
vg0805947641 T C 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
vg0805947641 NA 6.22E-06 mr1125 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
vg0805947641 NA 6.40E-07 mr1742 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
vg0805947641 NA 4.81E-12 mr1769 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
vg0805947641 5.13E-06 6.97E-09 mr1039_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
vg0805947641 5.26E-06 5.25E-06 mr1196_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
vg0805947641 NA 5.66E-07 mr1232_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
vg0805947641 NA 3.57E-08 mr1261_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
vg0805947641 1.91E-06 1.91E-06 mr1266_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
vg0805947641 NA 6.65E-09 mr1304_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
vg0805947641 NA 3.26E-07 mr1308_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
vg0805947641 6.25E-06 6.24E-06 mr1345_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
vg0805947641 NA 3.00E-08 mr1401_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
vg0805947641 NA 1.48E-06 mr1422_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
vg0805947641 2.47E-06 2.46E-06 mr1424_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
vg0805947641 NA 4.60E-08 mr1551_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
vg0805947641 NA 5.73E-06 mr1557_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
vg0805947641 NA 1.17E-06 mr1575_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
vg0805947641 NA 4.25E-09 mr1584_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
vg0805947641 NA 2.20E-08 mr1606_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
vg0805947641 4.33E-06 2.56E-09 mr1632_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
vg0805947641 NA 1.91E-06 mr1633_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
vg0805947641 NA 3.13E-07 mr1653_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
vg0805947641 NA 1.16E-07 mr1659_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
vg0805947641 NA 1.93E-08 mr1696_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
vg0805947641 NA 2.23E-06 mr1730_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
vg0805947641 NA 1.56E-06 mr1819_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
vg0805947641 6.25E-07 3.23E-09 mr1830_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
vg0805947641 6.97E-06 6.97E-06 mr1846_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
vg0805947641 6.49E-06 1.75E-06 mr1849_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
vg0805947641 NA 1.55E-06 mr1853_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
vg0805947641 NA 2.58E-07 mr1860_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
vg0805947641 NA 7.82E-09 mr1866_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
vg0805947641 NA 7.82E-08 mr1873_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
vg0805947641 NA 2.33E-06 mr1884_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
vg0805947641 2.61E-06 5.12E-10 mr1905_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
vg0805947641 NA 1.90E-11 mr1916_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
vg0805947641 7.00E-06 7.00E-06 mr1938_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
vg0805947641 NA 3.81E-10 mr1942_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
vg0805947641 NA 3.48E-06 mr1944_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
vg0805947641 4.55E-06 NA mr1976_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