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Detailed information for vg0805944662:

Variant ID: vg0805944662 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5944662
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


GCGACGCCCGGTGGCTAAACTGGCCTGCAACGTCTTATCTTCCGGGCTAGCAGGATGGTGGGTTGGTCTGCTAGCTTGCAAGCCTGGTTGTGAGTGGTGA[C/G]
ACTATGAAAAGGTCTGTGGTTCCTGCTTGCCCCTGCTAGTTCGGCGGCATGGGAGTACGAAGCGGAGGCGATCAGTAGTTGCATCTAGCGGCATGGCTAG

Reverse complement sequence

CTAGCCATGCCGCTAGATGCAACTACTGATCGCCTCCGCTTCGTACTCCCATGCCGCCGAACTAGCAGGGGCAAGCAGGAACCACAGACCTTTTCATAGT[G/C]
TCACCACTCACAACCAGGCTTGCAAGCTAGCAGACCAACCCACCATCCTGCTAGCCCGGAAGATAAGACGTTGCAGGCCAGTTTAGCCACCGGGCGTCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 26.50% 11.10% 1.27% 61.09% NA
All Indica  2759 3.00% 7.20% 1.52% 88.18% NA
All Japonica  1512 74.10% 20.20% 0.07% 5.62% NA
Aus  269 6.70% 0.00% 3.35% 89.96% NA
Indica I  595 3.50% 0.20% 0.50% 95.80% NA
Indica II  465 5.80% 33.30% 1.72% 59.14% NA
Indica III  913 1.10% 0.70% 1.97% 96.28% NA
Indica Intermediate  786 3.30% 4.80% 1.65% 90.20% NA
Temperate Japonica  767 94.00% 3.80% 0.13% 2.09% NA
Tropical Japonica  504 43.70% 49.00% 0.00% 7.34% NA
Japonica Intermediate  241 74.30% 12.40% 0.00% 13.28% NA
VI/Aromatic  96 2.10% 3.10% 6.25% 88.54% NA
Intermediate  90 32.20% 18.90% 2.22% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805944662 C -> G LOC_Os08g10240.1 upstream_gene_variant ; 3749.0bp to feature; MODIFIER silent_mutation Average:55.807; most accessible tissue: Minghui63 young leaf, score: 93.523 N N N N
vg0805944662 C -> G LOC_Os08g10244.1 intron_variant ; MODIFIER silent_mutation Average:55.807; most accessible tissue: Minghui63 young leaf, score: 93.523 N N N N
vg0805944662 C -> G LOC_Os08g10250 intragenic_variant ; MODIFIER silent_mutation Average:55.807; most accessible tissue: Minghui63 young leaf, score: 93.523 N N N N
vg0805944662 C -> DEL N N silent_mutation Average:55.807; most accessible tissue: Minghui63 young leaf, score: 93.523 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)
vg0805944662 C G 0.04 0.03 0.04 0.03 0.04 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805944662 NA 6.82E-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
vg0805944662 NA 3.22E-06 mr1471 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
vg0805944662 NA 2.40E-06 mr1502 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
vg0805944662 NA 5.62E-08 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
vg0805944662 NA 1.65E-09 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
vg0805944662 1.75E-06 7.82E-10 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
vg0805944662 NA 4.83E-06 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
vg0805944662 8.19E-06 8.19E-06 mr1266_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
vg0805944662 NA 7.10E-10 mr1364_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
vg0805944662 NA 4.85E-06 mr1398_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
vg0805944662 NA 5.53E-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
vg0805944662 NA 1.37E-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
vg0805944662 NA 3.75E-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
vg0805944662 NA 4.18E-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
vg0805944662 NA 4.80E-06 mr1600_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
vg0805944662 NA 1.03E-07 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
vg0805944662 3.37E-06 4.57E-10 mr1632_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
vg0805944662 NA 3.19E-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
vg0805944662 NA 6.09E-08 mr1676_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
vg0805944662 NA 8.41E-06 mr1682_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
vg0805944662 NA 4.54E-07 mr1696_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
vg0805944662 NA 3.96E-09 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
vg0805944662 NA 3.41E-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
vg0805944662 1.75E-06 8.82E-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
vg0805944662 NA 4.78E-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
vg0805944662 NA 1.42E-08 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
vg0805944662 NA 1.11E-07 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
vg0805944662 5.49E-06 4.00E-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
vg0805944662 NA 2.56E-12 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
vg0805944662 NA 8.47E-11 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
vg0805944662 NA 1.93E-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
vg0805944662 9.30E-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
vg0805944662 NA 2.47E-13 mr1993_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