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Detailed information for vg1004727190:

Variant ID: vg1004727190 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4727190
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGCGAGCGGGATGGAGTAGTCTACGAGCGACGGCGCAGCACAGAGTAGGAGGCAAACCCTAGATTGGTTTCGCGTATGTTGCGTGAAGTCACCGGCTC[G/A]
GTTTATATAGAGATAGGTCGCTTGATCAGGGCGCCCGCACGATCTCCACTCCGCTAACCGAACTGGATTAGTCGCGCGTAACTTATCCGGACTCCACGAA

Reverse complement sequence

TTCGTGGAGTCCGGATAAGTTACGCGCGACTAATCCAGTTCGGTTAGCGGAGTGGAGATCGTGCGGGCGCCCTGATCAAGCGACCTATCTCTATATAAAC[C/T]
GAGCCGGTGACTTCACGCAACATACGCGAAACCAATCTAGGGTTTGCCTCCTACTCTGTGCTGCGCCGTCGCTCGTAGACTACTCCATCCCGCTCGCCGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.50% 1.90% 1.65% 55.92% NA
All Indica  2759 19.60% 0.50% 2.28% 77.64% NA
All Japonica  1512 66.50% 4.70% 0.99% 27.78% NA
Aus  269 96.30% 0.00% 0.00% 3.72% NA
Indica I  595 43.40% 0.00% 1.68% 54.96% NA
Indica II  465 13.10% 0.00% 3.44% 83.44% NA
Indica III  913 6.80% 1.00% 1.53% 90.69% NA
Indica Intermediate  786 20.20% 0.60% 2.93% 76.21% NA
Temperate Japonica  767 87.20% 1.20% 0.52% 11.08% NA
Tropical Japonica  504 48.80% 1.60% 1.19% 48.41% NA
Japonica Intermediate  241 37.80% 22.40% 2.07% 37.76% NA
VI/Aromatic  96 67.70% 1.00% 0.00% 31.25% NA
Intermediate  90 51.10% 3.30% 0.00% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004727190 G -> A LOC_Os10g08702.1 downstream_gene_variant ; 4903.0bp to feature; MODIFIER silent_mutation Average:50.698; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 N N N N
vg1004727190 G -> A LOC_Os10g08710.1 downstream_gene_variant ; 902.0bp to feature; MODIFIER silent_mutation Average:50.698; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 N N N N
vg1004727190 G -> A LOC_Os10g08710-LOC_Os10g08720 intergenic_region ; MODIFIER silent_mutation Average:50.698; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 N N N N
vg1004727190 G -> DEL N N silent_mutation Average:50.698; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 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)
vg1004727190 G A -0.01 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004727190 NA 4.84E-06 mr1113 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
vg1004727190 1.14E-06 6.25E-09 mr1114 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
vg1004727190 1.99E-06 6.44E-09 mr1117 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
vg1004727190 NA 7.68E-09 mr1118 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
vg1004727190 2.94E-06 7.37E-08 mr1119 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
vg1004727190 NA 1.02E-06 mr1120 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
vg1004727190 4.20E-07 1.50E-09 mr1123 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
vg1004727190 2.84E-07 2.68E-10 mr1242 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
vg1004727190 8.83E-06 2.59E-07 mr1247 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
vg1004727190 NA 3.34E-07 mr1495 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
vg1004727190 9.89E-06 4.98E-08 mr1496 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
vg1004727190 NA 8.64E-07 mr1917 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
vg1004727190 NA 4.64E-07 mr1961 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
vg1004727190 8.23E-06 1.34E-07 mr1113_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
vg1004727190 1.26E-06 1.17E-08 mr1114_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
vg1004727190 1.54E-07 2.46E-10 mr1117_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
vg1004727190 5.79E-06 3.84E-08 mr1118_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
vg1004727190 8.30E-06 2.16E-08 mr1119_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
vg1004727190 7.12E-06 1.02E-07 mr1120_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
vg1004727190 3.04E-07 7.93E-09 mr1123_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
vg1004727190 8.65E-06 NA mr1150_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
vg1004727190 5.49E-09 4.00E-12 mr1240_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
vg1004727190 3.00E-08 7.17E-11 mr1242_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
vg1004727190 NA 1.89E-07 mr1247_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
vg1004727190 3.41E-07 7.77E-09 mr1495_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
vg1004727190 2.72E-09 5.14E-13 mr1496_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
vg1004727190 2.87E-06 2.45E-07 mr1936_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