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Detailed information for vg0609976964:

Variant ID: vg0609976964 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9976964
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGTCTCAATATATAAGAACCTAGGGCCGGATGGAATATTTCCTAGTACTCCACATTCGTAGTACTAGAAACGAATCTAAATAGACTGCTATCCAGATT[T/C]
ATAGTACTAGGAAATGTCTTATCTGATTCTAGTTCTTGTATATTAGGACGGAGGGAGTAGTAGTTTAGAACCAAGAAGACAAGAGCATGGGGCTTTCTGT

Reverse complement sequence

ACAGAAAGCCCCATGCTCTTGTCTTCTTGGTTCTAAACTACTACTCCCTCCGTCCTAATATACAAGAACTAGAATCAGATAAGACATTTCCTAGTACTAT[A/G]
AATCTGGATAGCAGTCTATTTAGATTCGTTTCTAGTACTACGAATGTGGAGTACTAGGAAATATTCCATCCGGCCCTAGGTTCTTATATATTGAGACGGA

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 66.70% 32.30% 0.08% 0.89% NA
All Indica  2759 69.40% 30.30% 0.11% 0.11% NA
All Japonica  1512 58.10% 41.90% 0.00% 0.00% NA
Aus  269 83.30% 3.00% 0.00% 13.75% NA
Indica I  595 86.90% 12.90% 0.17% 0.00% NA
Indica II  465 83.70% 16.30% 0.00% 0.00% NA
Indica III  913 57.90% 42.10% 0.00% 0.00% NA
Indica Intermediate  786 61.20% 38.20% 0.25% 0.38% NA
Temperate Japonica  767 46.80% 53.20% 0.00% 0.00% NA
Tropical Japonica  504 66.50% 33.50% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 9.40% 0.00% 2.08% NA
Intermediate  90 54.40% 44.40% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609976964 T -> C LOC_Os06g17210.1 upstream_gene_variant ; 4445.0bp to feature; MODIFIER silent_mutation Average:83.475; most accessible tissue: Callus, score: 98.155 N N N N
vg0609976964 T -> C LOC_Os06g17230.1 upstream_gene_variant ; 1233.0bp to feature; MODIFIER silent_mutation Average:83.475; most accessible tissue: Callus, score: 98.155 N N N N
vg0609976964 T -> C LOC_Os06g17220.1 downstream_gene_variant ; 84.0bp to feature; MODIFIER silent_mutation Average:83.475; most accessible tissue: Callus, score: 98.155 N N N N
vg0609976964 T -> C LOC_Os06g17220-LOC_Os06g17230 intergenic_region ; MODIFIER silent_mutation Average:83.475; most accessible tissue: Callus, score: 98.155 N N N N
vg0609976964 T -> DEL N N silent_mutation Average:83.475; most accessible tissue: Callus, score: 98.155 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)
vg0609976964 T C 0.02 -0.03 -0.03 -0.06 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609976964 3.00E-06 NA mr1068 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
vg0609976964 1.24E-09 NA mr1090 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
vg0609976964 8.39E-08 8.88E-08 mr1090 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
vg0609976964 2.82E-09 NA mr1211 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
vg0609976964 3.36E-10 6.81E-12 mr1211 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
vg0609976964 NA 2.06E-06 mr1218 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
vg0609976964 NA 2.06E-11 mr1221 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
vg0609976964 NA 8.61E-06 mr1352 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
vg0609976964 NA 1.78E-07 mr1422 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
vg0609976964 NA 2.27E-06 mr1534 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
vg0609976964 NA 1.63E-12 mr1583 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
vg0609976964 5.92E-08 NA mr1090_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
vg0609976964 1.14E-06 4.39E-08 mr1090_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
vg0609976964 1.07E-08 NA mr1211_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
vg0609976964 8.77E-09 1.30E-11 mr1211_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
vg0609976964 NA 4.27E-09 mr1218_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
vg0609976964 NA 9.12E-06 mr1220_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
vg0609976964 NA 2.58E-15 mr1221_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
vg0609976964 NA 8.57E-07 mr1242_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
vg0609976964 NA 4.39E-07 mr1422_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
vg0609976964 2.86E-06 2.86E-06 mr1571_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
vg0609976964 NA 1.02E-13 mr1583_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
vg0609976964 NA 8.11E-06 mr1654_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
vg0609976964 NA 1.57E-11 mr1850_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