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Detailed information for vg1209054055:

Variant ID: vg1209054055 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9054055
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.17, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:


ACAACTCCTCCTCGATATACATGAAGGCATCTGTGGGTCACATGCCGTCGGTCGCACATTGGTCGGGAAAGCCTTTCGACAAGGGTTTTTCTGGCCAACC[A/G]
CCCTCAAAGACGCATTTGACATAGTCCAGCGGTGTGAAGCCTGTCAATTCCACAGCAAGCACAGAAAGCTACCTACACAAGCGCTCCAGACCATCCCTCT

Reverse complement sequence

AGAGGGATGGTCTGGAGCGCTTGTGTAGGTAGCTTTCTGTGCTTGCTGTGGAATTGACAGGCTTCACACCGCTGGACTATGTCAAATGCGTCTTTGAGGG[T/C]
GGTTGGCCAGAAAAACCCTTGTCGAAAGGCTTTCCCGACCAATGTGCGACCGACGGCATGTGACCCACAGATGCCTTCATGTATATCGAGGAGGAGTTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.80% 36.40% 0.68% 11.15% NA
All Indica  2759 74.20% 6.50% 0.98% 18.38% NA
All Japonica  1512 4.50% 94.40% 0.13% 0.93% NA
Aus  269 95.90% 3.30% 0.74% 0.00% NA
Indica I  595 48.40% 8.40% 2.02% 41.18% NA
Indica II  465 65.40% 7.70% 1.08% 25.81% NA
Indica III  913 93.40% 3.00% 0.22% 3.40% NA
Indica Intermediate  786 76.50% 8.40% 1.02% 14.12% NA
Temperate Japonica  767 6.10% 92.60% 0.26% 1.04% NA
Tropical Japonica  504 3.60% 95.80% 0.00% 0.60% NA
Japonica Intermediate  241 1.20% 97.50% 0.00% 1.24% NA
VI/Aromatic  96 42.70% 54.20% 0.00% 3.12% NA
Intermediate  90 40.00% 55.60% 1.11% 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
vg1209054055 A -> DEL LOC_Os12g15900.1 N frameshift_variant Average:31.018; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N
vg1209054055 A -> G LOC_Os12g15900.1 missense_variant ; p.Thr622Ala; MODERATE nonsynonymous_codon ; T622V Average:31.018; most accessible tissue: Minghui63 flag leaf, score: 60.569 benign 0.182 DELETERIOUS 0.01
vg1209054055 A -> G LOC_Os12g15900.1 missense_variant ; p.Thr622Ala; MODERATE nonsynonymous_codon ; T622A Average:31.018; most accessible tissue: Minghui63 flag leaf, score: 60.569 benign -0.764 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209054055 NA 7.61E-06 mr1004 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
vg1209054055 NA 1.19E-08 mr1066 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
vg1209054055 NA 2.64E-19 mr1133 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
vg1209054055 NA 3.76E-07 mr1527 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
vg1209054055 NA 2.21E-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
vg1209054055 NA 1.55E-12 mr1553 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
vg1209054055 NA 1.63E-07 mr1574 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
vg1209054055 NA 2.54E-12 mr1623 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
vg1209054055 2.96E-06 2.96E-06 mr1623 Ind_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
vg1209054055 NA 6.93E-08 mr1659 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
vg1209054055 NA 8.04E-07 mr1781 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
vg1209054055 NA 5.07E-06 mr1002_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
vg1209054055 NA 3.78E-06 mr1020_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
vg1209054055 NA 1.99E-14 mr1133_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
vg1209054055 NA 3.30E-06 mr1574_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
vg1209054055 NA 2.43E-07 mr1582_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
vg1209054055 NA 2.76E-06 mr1870_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