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Detailed information for vg1117445573:

Variant ID: vg1117445573 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17445573
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATATGACTACTTTGACTTTGGATTCGCTTTACACAAAACTTAAAACACATGAGATGAATATTCTTGCTCGTAAAGTTGATTCTAAGTCTAGTGCTTT[T/G]
GTTTCTTCTTCGACCTCTTTGGATGTTGGTGCTTCTACATCAAAGTCTTCAATTCTTGCTTTAATTAATGCCACGTCCGAAGATCAACTCGAACAGTTCG

Reverse complement sequence

CGAACTGTTCGAGTTGATCTTCGGACGTGGCATTAATTAAAGCAAGAATTGAAGACTTTGATGTAGAAGCACCAACATCCAAAGAGGTCGAAGAAGAAAC[A/C]
AAAGCACTAGACTTAGAATCAACTTTACGAGCAAGAATATTCATCTCATGTGTTTTAAGTTTTGTGTAAAGCGAATCCAAAGTCAAAGTAGTCATATCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 10.30% 2.09% 2.22% NA
All Indica  2759 99.30% 0.40% 0.29% 0.00% NA
All Japonica  1512 55.90% 31.30% 5.89% 6.88% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.50% 1.20% 1.34% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 25.70% 51.20% 9.52% 13.56% NA
Tropical Japonica  504 96.80% 2.40% 0.79% 0.00% NA
Japonica Intermediate  241 66.40% 28.60% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117445573 T -> DEL LOC_Os11g30000.1 N frameshift_variant Average:29.565; most accessible tissue: Zhenshan97 young leaf, score: 43.23 N N N N
vg1117445573 T -> G LOC_Os11g30000.1 missense_variant ; p.Phe232Leu; MODERATE nonsynonymous_codon ; F232L Average:29.565; most accessible tissue: Zhenshan97 young leaf, score: 43.23 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117445573 3.62E-06 NA Awn_length 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
vg1117445573 2.34E-06 NA mr1354 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
vg1117445573 NA 9.92E-06 mr1882 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
vg1117445573 NA 8.05E-06 mr1910 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
vg1117445573 5.61E-06 NA mr1115_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
vg1117445573 1.41E-10 6.97E-35 mr1137_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
vg1117445573 5.38E-06 3.92E-11 mr1137_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
vg1117445573 4.77E-07 NA mr1354_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
vg1117445573 NA 5.15E-06 mr1555_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
vg1117445573 1.43E-07 NA mr1617_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
vg1117445573 NA 7.67E-08 mr1617_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