Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0401599517:

Variant ID: vg0401599517 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1599517
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTCGGCCTTGGTCGATCACCTGGACCTATGTCTATTTCTTCTAAATCATCAGTCGACATGAAACCTTGTCCTTGCTTGTCATCGAGATCATCTACTAT[G/A]
TCCTTGGTGTAGACGTTTGAACCCTCCACGACGCCCTCAAAGTAATAGCTTGGGTTCTCCATCTTCAATCGGCTGTATATCAGAATCGGACACTTTTAGA

Reverse complement sequence

TCTAAAAGTGTCCGATTCTGATATACAGCCGATTGAAGATGGAGAACCCAAGCTATTACTTTGAGGGCGTCGTGGAGGGTTCAAACGTCTACACCAAGGA[C/T]
ATAGTAGATGATCTCGATGACAAGCAAGGACAAGGTTTCATGTCGACTGATGATTTAGAAGAAATAGACATAGGTCCAGGTGATCGACCAAGGCCGACAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.80% 30.20% 3.13% 4.80% NA
All Indica  2759 72.70% 23.80% 3.08% 0.36% NA
All Japonica  1512 41.80% 41.50% 2.65% 14.09% NA
Aus  269 65.40% 31.60% 2.97% 0.00% NA
Indica I  595 59.30% 38.00% 2.35% 0.34% NA
Indica II  465 90.30% 6.90% 2.37% 0.43% NA
Indica III  913 73.60% 22.20% 3.83% 0.33% NA
Indica Intermediate  786 71.40% 25.10% 3.18% 0.38% NA
Temperate Japonica  767 12.30% 64.30% 2.22% 21.25% NA
Tropical Japonica  504 87.30% 8.30% 2.38% 1.98% NA
Japonica Intermediate  241 40.70% 38.20% 4.56% 16.60% NA
VI/Aromatic  96 63.50% 30.20% 5.21% 1.04% NA
Intermediate  90 53.30% 32.20% 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
vg0401599517 G -> DEL LOC_Os04g03630.1 N frameshift_variant Average:28.619; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N
vg0401599517 G -> A LOC_Os04g03630.1 synonymous_variant ; p.Asp1119Asp; LOW synonymous_codon Average:28.619; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401599517 1.59E-06 NA Spikelet_length Ind_All YES 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
vg0401599517 NA 2.21E-06 mr1013 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
vg0401599517 NA 1.01E-06 mr1031 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
vg0401599517 NA 3.25E-06 mr1056 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
vg0401599517 NA 1.14E-06 mr1156 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
vg0401599517 NA 1.55E-06 mr1252 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
vg0401599517 NA 7.62E-06 mr1614 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
vg0401599517 NA 2.45E-06 mr1621 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
vg0401599517 7.65E-06 7.62E-06 mr1703 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
vg0401599517 NA 2.09E-10 mr1769 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
vg0401599517 NA 1.47E-06 mr1887 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
vg0401599517 NA 5.04E-07 mr1013_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