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Detailed information for vg0805873180:

Variant ID: vg0805873180 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5873180
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.35, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTTCTTGTTGTTGTGGGATGCATGAGGATTCTTCTTCTGTACCATATTGGCACTAGAACCTCCCTCAACCTTTTTGCCCCGGTTGTCCTTTGCCCTCG[T/C]
CTTCTCTTCAACACCCAAAGAGCCAATGAGATCAGAAACACTGAACTCTTGTCTCTTGTGCTTTAGAGAAGTGGCAAAGTCCGACCAAGAAGGTGGCAAT

Reverse complement sequence

ATTGCCACCTTCTTGGTCGGACTTTGCCACTTCTCTAAAGCACAAGAGACAAGAGTTCAGTGTTTCTGATCTCATTGGCTCTTTGGGTGTTGAAGAGAAG[A/G]
CGAGGGCAAAGGACAACCGGGGCAAAAAGGTTGAGGGAGGTTCTAGTGCCAATATGGTACAGAAGAAGAATCCTCATGCATCCCACAACAACAAGAAAGT

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 64.20% 34.70% 0.66% 0.42% NA
All Indica  2759 93.90% 5.50% 0.65% 0.00% NA
All Japonica  1512 3.80% 94.20% 0.66% 1.32% NA
Aus  269 91.40% 7.40% 1.12% 0.00% NA
Indica I  595 88.70% 10.10% 1.18% 0.00% NA
Indica II  465 92.90% 6.50% 0.65% 0.00% NA
Indica III  913 98.60% 1.30% 0.11% 0.00% NA
Indica Intermediate  786 92.90% 6.20% 0.89% 0.00% NA
Temperate Japonica  767 1.80% 97.80% 0.00% 0.39% NA
Tropical Japonica  504 6.20% 92.70% 0.40% 0.79% NA
Japonica Intermediate  241 5.00% 86.30% 3.32% 5.39% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 0.00% 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
vg0805873180 T -> C LOC_Os08g10120.1 missense_variant ; p.Thr138Ala; MODERATE nonsynonymous_codon ; T138A Average:18.066; most accessible tissue: Minghui63 flag leaf, score: 39.69 benign -1.469 TOLERATED 1.00
vg0805873180 T -> DEL LOC_Os08g10120.1 N frameshift_variant Average:18.066; most accessible tissue: Minghui63 flag leaf, score: 39.69 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805873180 NA 4.13E-10 Grain_weight 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
vg0805873180 NA 5.39E-23 mr1588 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
vg0805873180 NA 3.02E-29 mr1638 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
vg0805873180 NA 2.67E-37 mr1828 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
vg0805873180 NA 1.99E-35 mr1932 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
vg0805873180 NA 2.94E-75 mr1934 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
vg0805873180 NA 2.98E-51 mr1935 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
vg0805873180 NA 8.62E-09 mr1050_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
vg0805873180 NA 1.74E-53 mr1141_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
vg0805873180 NA 7.58E-35 mr1223_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
vg0805873180 NA 3.63E-24 mr1350_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
vg0805873180 NA 4.68E-61 mr1402_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
vg0805873180 NA 1.12E-33 mr1448_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
vg0805873180 NA 2.01E-27 mr1588_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
vg0805873180 NA 6.02E-48 mr1721_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
vg0805873180 NA 1.46E-74 mr1828_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
vg0805873180 NA 1.90E-82 mr1934_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