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Detailed information for vg0411710445:

Variant ID: vg0411710445 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11710445
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.17, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTTGGGAGGAAGCCTAATGTCGTCTATTTTCAAGTTTTTGGTTGCAAGTGTTATATTTACCGAAAGGGTGTTAGACTAACCAAATTTGAAAGTCGGTG[C/T]
GATGAAGGGTTTCTTCTAGGTTATGCCTCAAATAGCAAGGCATACCGGGTCTACAACAAGAACAAAAGTATTGTGGAAGAAACCGACGATGTTCAATTTG

Reverse complement sequence

CAAATTGAACATCGTCGGTTTCTTCCACAATACTTTTGTTCTTGTTGTAGACCCGGTATGCCTTGCTATTTGAGGCATAACCTAGAAGAAACCCTTCATC[G/A]
CACCGACTTTCAAATTTGGTTAGTCTAACACCCTTTCGGTAAATATAACACTTGCAACCAAAAACTTGAAAATAGACGACATTAGGCTTCCTCCCAACAA

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 30.10% 0.30% 8.99% 60.60% NA
All Indica  2759 2.10% 0.40% 8.92% 88.58% NA
All Japonica  1512 87.50% 0.00% 2.45% 10.05% NA
Aus  269 0.40% 1.50% 30.86% 67.29% NA
Indica I  595 1.00% 0.30% 1.01% 97.65% NA
Indica II  465 4.50% 0.40% 13.12% 81.94% NA
Indica III  913 1.50% 0.50% 13.58% 84.34% NA
Indica Intermediate  786 2.30% 0.10% 7.00% 90.59% NA
Temperate Japonica  767 91.50% 0.00% 0.39% 8.08% NA
Tropical Japonica  504 90.10% 0.00% 2.78% 7.14% NA
Japonica Intermediate  241 69.30% 0.00% 8.30% 22.41% NA
VI/Aromatic  96 7.30% 0.00% 51.04% 41.67% NA
Intermediate  90 36.70% 0.00% 11.11% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0411710445 C -> DEL LOC_Os04g20860.1 N frameshift_variant Average:12.044; most accessible tissue: Callus, score: 26.675 N N N N
vg0411710445 C -> T LOC_Os04g20860.1 synonymous_variant ; p.Cys184Cys; LOW synonymous_codon Average:12.044; most accessible tissue: Callus, score: 26.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411710445 NA 5.17E-90 mr1071 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
vg0411710445 NA 3.96E-07 mr1245 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
vg0411710445 NA 1.69E-15 mr1276 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
vg0411710445 NA 3.61E-28 mr1298 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
vg0411710445 NA 7.00E-17 mr1324 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
vg0411710445 NA 3.29E-13 mr1335 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
vg0411710445 1.59E-06 NA mr1343 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
vg0411710445 NA 1.70E-66 mr1619 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
vg0411710445 NA 7.64E-08 mr1690 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
vg0411710445 NA 6.53E-10 mr1714 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
vg0411710445 NA 4.02E-18 mr1715 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
vg0411710445 NA 5.33E-10 mr1806 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
vg0411710445 1.90E-06 NA mr1829 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
vg0411710445 5.06E-07 NA mr1842 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
vg0411710445 NA 1.25E-17 mr1968 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
vg0411710445 NA 2.72E-20 mr1298_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
vg0411710445 NA 8.00E-16 mr1416_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
vg0411710445 NA 1.80E-06 mr1549_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
vg0411710445 NA 5.78E-15 mr1686_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
vg0411710445 NA 7.61E-10 mr1806_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
vg0411710445 7.47E-06 NA mr1829_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