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Detailed information for vg0113847918:

Variant ID: vg0113847918 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13847918
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACAAGCATTCATTTCATTAATTAATCTCTCAAACGCAAGTACGTATAACTCGACAATTATTCCTTATTCCACGTGAGGAATTAACGGGAGGGATAAGAG[G/A]
AAGAGAAGATGCTAGAGGGGGAGGACGACGCCAGTGGCAATCGAGGTCGACGAGGTGGCCGGCTAGCTAGCTACTAGACGGTGGGGTAGAAAGGTGAGAC

Reverse complement sequence

GTCTCACCTTTCTACCCCACCGTCTAGTAGCTAGCTAGCCGGCCACCTCGTCGACCTCGATTGCCACTGGCGTCGTCCTCCCCCTCTAGCATCTTCTCTT[C/T]
CTCTTATCCCTCCCGTTAATTCCTCACGTGGAATAAGGAATAATTGTCGAGTTATACGTACTTGCGTTTGAGAGATTAATTAATGAAATGAATGCTTGTT

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 82.60% 14.10% 0.15% 3.13% NA
All Indica  2759 85.20% 13.00% 0.07% 1.70% NA
All Japonica  1512 92.50% 2.10% 0.26% 5.09% NA
Aus  269 12.30% 87.40% 0.00% 0.37% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 98.90% 0.60% 0.00% 0.43% NA
Indica III  913 71.70% 23.20% 0.22% 4.82% NA
Indica Intermediate  786 84.90% 15.00% 0.00% 0.13% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 80.80% 6.00% 0.79% 12.50% NA
Japonica Intermediate  241 93.40% 0.80% 0.00% 5.81% NA
VI/Aromatic  96 52.10% 26.00% 1.04% 20.83% NA
Intermediate  90 81.10% 15.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113847918 G -> A LOC_Os01g24560.1 downstream_gene_variant ; 4169.0bp to feature; MODIFIER silent_mutation Average:70.626; most accessible tissue: Minghui63 root, score: 84.323 N N N N
vg0113847918 G -> A LOC_Os01g24570.1 downstream_gene_variant ; 74.0bp to feature; MODIFIER silent_mutation Average:70.626; most accessible tissue: Minghui63 root, score: 84.323 N N N N
vg0113847918 G -> A LOC_Os01g24560-LOC_Os01g24570 intergenic_region ; MODIFIER silent_mutation Average:70.626; most accessible tissue: Minghui63 root, score: 84.323 N N N N
vg0113847918 G -> DEL N N silent_mutation Average:70.626; most accessible tissue: Minghui63 root, score: 84.323 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113847918 NA 2.33E-06 mr1028 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
vg0113847918 NA 8.82E-25 mr1095 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
vg0113847918 NA 7.05E-29 mr1098 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
vg0113847918 NA 2.27E-14 mr1180 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
vg0113847918 NA 1.29E-06 mr1180 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
vg0113847918 NA 2.26E-13 mr1183 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
vg0113847918 NA 6.16E-22 mr1210 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
vg0113847918 NA 1.27E-12 mr1503 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
vg0113847918 NA 1.32E-25 mr1586 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
vg0113847918 NA 2.09E-23 mr1589 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
vg0113847918 NA 2.35E-08 mr1660 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
vg0113847918 1.68E-06 2.18E-07 mr1739 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
vg0113847918 NA 1.07E-12 mr1739 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
vg0113847918 NA 3.76E-17 mr1765 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
vg0113847918 NA 2.39E-25 mr1868 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
vg0113847918 NA 2.61E-18 mr1911 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
vg0113847918 NA 2.29E-15 mr1918 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
vg0113847918 NA 4.75E-06 mr1931 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
vg0113847918 NA 6.96E-22 mr1095_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
vg0113847918 NA 5.45E-16 mr1180_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
vg0113847918 NA 2.24E-06 mr1180_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
vg0113847918 NA 6.14E-20 mr1305_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
vg0113847918 NA 7.91E-06 mr1360_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
vg0113847918 NA 6.69E-12 mr1409_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
vg0113847918 NA 1.37E-09 mr1739_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
vg0113847918 NA 1.11E-10 mr1739_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
vg0113847918 NA 9.61E-16 mr1794_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