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Detailed information for vg1017965135:

Variant ID: vg1017965135 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17965135
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.35, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CCCCACCCCACGAAAACCGATGGCGACATGTCTCCTCCCATTTAATTCCCATGGTGAACCAATTCTAATTATCCCCGTCCCCTAATGGGTGAATTCACCG[T/C]
GGAGAAACGGTGAATGGGGCACCACTGCCATCTCTAGGACTATCATAGAAAAAAAAACTCAAATTCCGCATATATTTGTGTGTGTGTGTGGGGTGTTGTT

Reverse complement sequence

AACAACACCCCACACACACACACAAATATATGCGGAATTTGAGTTTTTTTTTCTATGATAGTCCTAGAGATGGCAGTGGTGCCCCATTCACCGTTTCTCC[A/G]
CGGTGAATTCACCCATTAGGGGACGGGGATAATTAGAATTGGTTCACCATGGGAATTAAATGGGAGGAGACATGTCGCCATCGGTTTTCGTGGGGTGGGG

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 58.30% 35.60% 6.12% 0.00% NA
All Indica  2759 75.50% 14.70% 9.82% 0.00% NA
All Japonica  1512 22.20% 77.20% 0.53% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 77.50% 1.80% 20.67% 0.00% NA
Indica II  465 72.90% 19.10% 7.96% 0.00% NA
Indica III  913 74.90% 23.00% 2.08% 0.00% NA
Indica Intermediate  786 76.20% 12.10% 11.70% 0.00% NA
Temperate Japonica  767 2.20% 97.50% 0.26% 0.00% NA
Tropical Japonica  504 41.30% 58.30% 0.40% 0.00% NA
Japonica Intermediate  241 46.10% 52.30% 1.66% 0.00% NA
VI/Aromatic  96 26.00% 72.90% 1.04% 0.00% NA
Intermediate  90 48.90% 41.10% 10.00% 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
vg1017965135 T -> C LOC_Os10g33840.1 upstream_gene_variant ; 649.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33855.1 upstream_gene_variant ; 2549.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33840.3 upstream_gene_variant ; 649.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33840.2 upstream_gene_variant ; 649.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33855.2 upstream_gene_variant ; 2555.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33850.1 downstream_gene_variant ; 752.0bp to feature; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 N N N N
vg1017965135 T -> C LOC_Os10g33840-LOC_Os10g33850 intergenic_region ; MODIFIER silent_mutation Average:88.815; most accessible tissue: Zhenshan97 flag leaf, score: 94.853 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)
vg1017965135 T C 0.03 0.02 0.03 0.02 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017965135 NA 1.91E-13 mr1239 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
vg1017965135 NA 1.80E-09 mr1277 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
vg1017965135 NA 1.09E-08 mr1794 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
vg1017965135 6.37E-06 6.37E-06 mr1929 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
vg1017965135 NA 4.19E-07 mr1045_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
vg1017965135 NA 6.46E-40 mr1072_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
vg1017965135 NA 5.55E-39 mr1075_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
vg1017965135 NA 7.03E-26 mr1077_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
vg1017965135 NA 2.46E-31 mr1149_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
vg1017965135 NA 7.69E-07 mr1222_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
vg1017965135 NA 2.62E-08 mr1299_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
vg1017965135 NA 6.90E-33 mr1441_2 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
vg1017965135 NA 3.45E-09 mr1482_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
vg1017965135 NA 1.36E-12 mr1537_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
vg1017965135 NA 6.57E-19 mr1592_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
vg1017965135 NA 4.09E-10 mr1595_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
vg1017965135 NA 7.68E-10 mr1600_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
vg1017965135 NA 1.07E-07 mr1727_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
vg1017965135 NA 8.80E-09 mr1741_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
vg1017965135 NA 6.82E-06 mr1751_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
vg1017965135 NA 1.11E-07 mr1783_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
vg1017965135 NA 5.38E-06 mr1785_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
vg1017965135 NA 4.02E-06 mr1788_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
vg1017965135 NA 2.09E-14 mr1790_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
vg1017965135 NA 1.09E-07 mr1804_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
vg1017965135 NA 2.35E-07 mr1837_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
vg1017965135 NA 9.02E-06 mr1840_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
vg1017965135 NA 7.44E-06 mr1929_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