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Detailed information for vg0315818553:

Variant ID: vg0315818553 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15818553
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCCTTTTCCTTCTAATTGGTTCAGATTGATGCAATTTGTTTCATACTTACTATGAATAAGGTCTTGTTTAGTTGGAAAAAAATTTTGGTTTTGGTTGT[C/T]
ACATCGGATATACGGACACACATTTGAAGTATTAAACGTAGTCTAATAACAAAACAAATTATAGATTCCGTCAGAAAACTGCGAGACAAATTTATTAAGC

Reverse complement sequence

GCTTAATAAATTTGTCTCGCAGTTTTCTGACGGAATCTATAATTTGTTTTGTTATTAGACTACGTTTAATACTTCAAATGTGTGTCCGTATATCCGATGT[G/A]
ACAACCAAAACCAAAATTTTTTTCCAACTAAACAAGACCTTATTCATAGTAAGTATGAAACAAATTGCATCAATCTGAACCAATTAGAAGGAAAAGGCCA

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 34.10% 8.30% 6.88% 50.72% NA
All Indica  2759 11.30% 11.80% 7.58% 69.26% NA
All Japonica  1512 67.10% 4.00% 7.34% 21.56% NA
Aus  269 63.20% 0.40% 0.74% 35.69% NA
Indica I  595 2.20% 7.60% 5.88% 84.37% NA
Indica II  465 12.70% 7.30% 4.09% 75.91% NA
Indica III  913 19.50% 18.50% 11.61% 50.38% NA
Indica Intermediate  786 8.00% 9.90% 6.23% 75.83% NA
Temperate Japonica  767 96.00% 0.30% 0.91% 2.87% NA
Tropical Japonica  504 21.40% 8.70% 17.46% 52.38% NA
Japonica Intermediate  241 71.00% 5.80% 6.64% 16.60% NA
VI/Aromatic  96 80.20% 1.00% 1.04% 17.71% NA
Intermediate  90 38.90% 6.70% 2.22% 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
vg0315818553 C -> T LOC_Os03g27580-LOC_Os03g27590 intergenic_region ; MODIFIER silent_mutation Average:18.218; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg0315818553 C -> DEL N N silent_mutation Average:18.218; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315818553 5.56E-06 6.50E-17 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0315818553 4.68E-06 1.48E-06 mr1324 Ind_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
vg0315818553 NA 9.47E-06 mr1325 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
vg0315818553 3.35E-06 2.04E-06 mr1335 Ind_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
vg0315818553 NA 7.42E-20 mr1422 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
vg0315818553 NA 1.90E-06 mr1502 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
vg0315818553 NA 1.19E-06 mr1629 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
vg0315818553 NA 5.10E-08 mr1733 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
vg0315818553 NA 1.35E-07 mr1951 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
vg0315818553 4.65E-06 NA mr1064_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
vg0315818553 NA 4.33E-08 mr1422_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
vg0315818553 NA 1.51E-06 mr1606_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