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Detailed information for vg0709163089:

Variant ID: vg0709163089 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9163089
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, A: 0.16, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGACCTAACCCTTTTTATCTTTCTGTCAAGTTGATTTTCAACTTCTGCCTTATAAATTTTAAAATAGTCTAGAGCTTCGTCTTTCGTTTTCAACAAGT[T/A]
CACATAGCAAAATCTAGTAGCATCATCAATCAACGTCATGAAATATCGTTTTCCACCCTTCGTCAACACCCCATTCATTTCACAAAGATCTGAATGTAGG

Reverse complement sequence

CCTACATTCAGATCTTTGTGAAATGAATGGGGTGTTGACGAAGGGTGGAAAACGATATTTCATGACGTTGATTGATGATGCTACTAGATTTTGCTATGTG[A/T]
ACTTGTTGAAAACGAAAGACGAAGCTCTAGACTATTTTAAAATTTATAAGGCAGAAGTTGAAAATCAACTTGACAGAAAGATAAAAAGGGTTAGGTCTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.30% 6.20% 6.94% 48.65% NA
All Indica  2759 4.50% 8.80% 8.84% 77.85% NA
All Japonica  1512 92.50% 1.80% 3.17% 2.58% NA
Aus  269 68.40% 1.90% 1.86% 27.88% NA
Indica I  595 4.20% 2.20% 5.38% 88.24% NA
Indica II  465 5.80% 9.90% 12.26% 72.04% NA
Indica III  913 2.30% 8.50% 9.64% 79.52% NA
Indica Intermediate  786 6.50% 13.50% 8.52% 71.50% NA
Temperate Japonica  767 94.30% 2.10% 0.13% 3.52% NA
Tropical Japonica  504 88.90% 2.00% 8.73% 0.40% NA
Japonica Intermediate  241 94.20% 0.40% 1.24% 4.15% NA
VI/Aromatic  96 63.50% 7.30% 27.08% 2.08% NA
Intermediate  90 45.60% 10.00% 5.56% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0709163089 T -> DEL LOC_Os07g15780.1 N frameshift_variant Average:10.56; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N
vg0709163089 T -> A LOC_Os07g15780.1 missense_variant ; p.Asn379Tyr; MODERATE nonsynonymous_codon Average:10.56; most accessible tissue: Zhenshan97 panicle, score: 20.424 probably damaging -2.295 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709163089 NA 3.72E-11 Heading_date Ind_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
vg0709163089 NA 2.59E-08 mr1045 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
vg0709163089 NA 5.35E-14 mr1170 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
vg0709163089 NA 2.25E-10 mr1175 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
vg0709163089 NA 6.89E-12 mr1316 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
vg0709163089 NA 4.35E-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
vg0709163089 NA 8.58E-06 mr1561 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
vg0709163089 NA 3.81E-06 mr1074_2 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
vg0709163089 NA 2.14E-06 mr1520_2 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
vg0709163089 NA 9.07E-06 mr1561_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
vg0709163089 NA 2.58E-07 mr1875_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
vg0709163089 NA 2.50E-06 mr1908_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