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Detailed information for vg1120464509:

Variant ID: vg1120464509 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20464509
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTGGTTCCAAGACAGGGGAGGCGGATGATGCAGAGATTGCAATTAAGAGATCGCTCCAGTTAAACCCCAACAACCCTACAATGGAGCTGGAGAAGGTA[T/A]
AACTATCTATTCTGCTCCACACATAATTTCAAGCAAATTCATTTGACTGCCTTACAATAATCTTGCTTGGTTTTCTTCTCTCTTTTTTTAATACTGAAAT

Reverse complement sequence

ATTTCAGTATTAAAAAAAGAGAGAAGAAAACCAAGCAAGATTATTGTAAGGCAGTCAAATGAATTTGCTTGAAATTATGTGTGGAGCAGAATAGATAGTT[A/T]
TACCTTCTCCAGCTCCATTGTAGGGTTGTTGGGGTTTAACTGGAGCGATCTCTTAATTGCAATCTCTGCATCATCCGCCTCCCCTGTCTTGGAACCAAAA

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 72.70% 4.30% 0.68% 22.28% NA
All Indica  2759 68.90% 0.20% 0.83% 30.05% NA
All Japonica  1512 81.70% 12.60% 0.00% 5.62% NA
Aus  269 53.20% 0.00% 2.60% 44.24% NA
Indica I  595 52.10% 0.30% 1.01% 46.55% NA
Indica II  465 79.60% 0.00% 1.29% 19.14% NA
Indica III  913 67.40% 0.30% 0.22% 32.09% NA
Indica Intermediate  786 77.10% 0.10% 1.15% 21.63% NA
Temperate Japonica  767 72.80% 23.20% 0.00% 4.04% NA
Tropical Japonica  504 89.10% 1.00% 0.00% 9.92% NA
Japonica Intermediate  241 95.00% 3.30% 0.00% 1.66% NA
VI/Aromatic  96 85.40% 0.00% 1.04% 13.54% NA
Intermediate  90 83.30% 7.80% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1120464509 T -> A LOC_Os11g34920.1 stop_lost ; p.Ter915Lysext*?; HIGH stop_lost Average:50.063; most accessible tissue: Callus, score: 87.38 N N N N
vg1120464509 T -> DEL LOC_Os11g34920.1 N frameshift_variant Average:50.063; most accessible tissue: Callus, score: 87.38 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120464509 NA 3.61E-10 Heading_date 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
vg1120464509 NA 1.76E-06 mr1354 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
vg1120464509 NA 2.63E-08 mr1031_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
vg1120464509 2.19E-06 2.19E-06 mr1193_2 Jap_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
vg1120464509 7.52E-06 1.54E-07 mr1321_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
vg1120464509 NA 4.06E-06 mr1321_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
vg1120464509 NA 5.00E-07 mr1354_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
vg1120464509 NA 2.49E-06 mr1371_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
vg1120464509 1.11E-07 NA mr1517_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
vg1120464509 NA 1.64E-07 mr1517_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
vg1120464509 8.88E-06 NA mr1539_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
vg1120464509 NA 4.26E-06 mr1567_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
vg1120464509 3.14E-06 7.33E-08 mr1577_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
vg1120464509 NA 7.67E-07 mr1577_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
vg1120464509 5.68E-06 NA mr1679_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
vg1120464509 NA 2.75E-07 mr1723_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
vg1120464509 4.65E-09 NA mr1768_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
vg1120464509 NA 7.02E-08 mr1768_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
vg1120464509 NA 4.17E-06 mr1792_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
vg1120464509 NA 2.72E-06 mr1829_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
vg1120464509 NA 9.69E-06 mr1865_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
vg1120464509 NA 3.25E-07 mr1902_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
vg1120464509 NA 6.05E-06 mr1977_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