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Detailed information for vg0905464468:

Variant ID: vg0905464468 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5464468
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCAACAAGTTTGCGCCGCTTTCGAGCCACTAAGTGATGTAGATGGTGAAAGTGGAGATGATGATAAGGGAAAGAACGTCTCCGATGTGTGCTTCATGG[T/C]
GCGTGGTGAATCTGACACAGAGTATGAAGATAATGAGGTGTGTGCTTTTGAAGAAGCTATTAATATTTTGAGTGCAAAAAATAAAAAGTGTGAGAAGATA

Reverse complement sequence

TATCTTCTCACACTTTTTATTTTTTGCACTCAAAATATTAATAGCTTCTTCAAAAGCACACACCTCATTATCTTCATACTCTGTGTCAGATTCACCACGC[A/G]
CCATGAAGCACACATCGGAGACGTTCTTTCCCTTATCATCATCTCCACTTTCACCATCTACATCACTTAGTGGCTCGAAAGCGGCGCAAACTTGTTGAAA

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 55.10% 30.10% 5.84% 8.97% NA
All Indica  2759 90.00% 3.00% 4.24% 2.72% NA
All Japonica  1512 1.10% 80.70% 1.72% 16.47% NA
Aus  269 19.00% 24.20% 22.68% 34.20% NA
Indica I  595 92.60% 2.50% 1.34% 3.53% NA
Indica II  465 92.90% 0.90% 3.66% 2.58% NA
Indica III  913 91.90% 3.50% 4.05% 0.55% NA
Indica Intermediate  786 84.10% 4.20% 7.00% 4.71% NA
Temperate Japonica  767 0.90% 89.60% 0.39% 9.13% NA
Tropical Japonica  504 1.00% 81.90% 2.98% 14.09% NA
Japonica Intermediate  241 2.10% 49.80% 3.32% 44.81% NA
VI/Aromatic  96 12.50% 17.70% 64.58% 5.21% NA
Intermediate  90 43.30% 42.20% 11.11% 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
vg0905464468 T -> DEL LOC_Os09g10030.1 N frameshift_variant Average:22.333; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0905464468 T -> C LOC_Os09g10030.1 missense_variant ; p.Val366Ala; MODERATE nonsynonymous_codon ; V366A Average:22.333; most accessible tissue: Minghui63 panicle, score: 29.741 benign -0.382 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905464468 NA 5.11E-22 mr1020 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
vg0905464468 NA 2.63E-21 mr1021 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
vg0905464468 NA 1.93E-12 mr1034 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
vg0905464468 NA 5.00E-16 mr1323 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
vg0905464468 NA 5.43E-12 mr1325 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
vg0905464468 NA 3.44E-14 mr1326 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
vg0905464468 NA 3.12E-14 mr1361 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
vg0905464468 NA 8.95E-22 mr1477 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
vg0905464468 NA 8.86E-06 mr1532 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
vg0905464468 NA 2.87E-10 mr1623 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
vg0905464468 NA 4.95E-15 mr1744 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
vg0905464468 NA 8.66E-22 mr1971 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
vg0905464468 NA 2.07E-21 mr1010_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
vg0905464468 NA 4.92E-09 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
vg0905464468 NA 2.01E-26 mr1323_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
vg0905464468 NA 6.59E-09 mr1700_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