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Detailed information for vg1222921847:

Variant ID: vg1222921847 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22921847
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGTCCAAGTGGAAACCCGTTTATTGCATATCAATTAAATAGTTTTAAAATTATTAATAACTGGTTAATTTGTAAGTATCACTTCAAAATATGTAACTT[T/C]
AAATTCAGCTTTATTTTTTTATAATTAATTATAAAAATTGAATTTAAGCTAGCACATTTATAAAGTAATATATAAATGCATATATTGTTAGGTTTTTTTT

Reverse complement sequence

AAAAAAAACCTAACAATATATGCATTTATATATTACTTTATAAATGTGCTAGCTTAAATTCAATTTTTATAATTAATTATAAAAAAATAAAGCTGAATTT[A/G]
AAGTTACATATTTTGAAGTGATACTTACAAATTAACCAGTTATTAATAATTTTAAAACTATTTAATTGATATGCAATAAACGGGTTTCCACTTGGACGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.40% 11.40% 6.20% 0.00% NA
All Indica  2759 95.30% 0.90% 3.84% 0.00% NA
All Japonica  1512 55.50% 33.10% 11.44% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 83.70% 1.70% 14.62% 0.00% NA
Indica II  465 97.00% 2.20% 0.86% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 97.80% 0.40% 1.78% 0.00% NA
Temperate Japonica  767 27.50% 56.60% 15.91% 0.00% NA
Tropical Japonica  504 90.10% 5.20% 4.76% 0.00% NA
Japonica Intermediate  241 72.20% 16.60% 11.20% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 75.60% 14.40% 10.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1222921847 T -> C LOC_Os12g37330.1 upstream_gene_variant ; 3057.0bp to feature; MODIFIER silent_mutation Average:40.583; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1222921847 T -> C LOC_Os12g37320.1 intron_variant ; MODIFIER silent_mutation Average:40.583; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1222921847 T -> C LOC_Os12g37320.2 intron_variant ; MODIFIER silent_mutation Average:40.583; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222921847 NA 7.73E-06 mr1010 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
vg1222921847 NA 9.18E-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
vg1222921847 NA 3.64E-06 mr1045 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
vg1222921847 2.47E-06 8.64E-10 mr1069 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
vg1222921847 NA 7.60E-06 mr1072 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
vg1222921847 NA 8.07E-08 mr1077 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
vg1222921847 7.49E-06 NA mr1137 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
vg1222921847 NA 2.65E-11 mr1137 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
vg1222921847 NA 5.57E-07 mr1149 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
vg1222921847 NA 5.33E-07 mr1163 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
vg1222921847 NA 1.14E-07 mr1164 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
vg1222921847 NA 5.31E-07 mr1202 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
vg1222921847 NA 1.26E-09 mr1330 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
vg1222921847 NA 6.68E-06 mr1441 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
vg1222921847 NA 8.50E-06 mr1482 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
vg1222921847 NA 7.50E-07 mr1503 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
vg1222921847 NA 4.41E-06 mr1576 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
vg1222921847 NA 5.30E-06 mr1576 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
vg1222921847 NA 2.61E-06 mr1596 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
vg1222921847 NA 4.66E-07 mr1596 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
vg1222921847 NA 2.16E-08 mr1617 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
vg1222921847 6.24E-06 NA mr1627 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
vg1222921847 NA 6.98E-10 mr1627 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
vg1222921847 NA 1.07E-06 mr1629 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
vg1222921847 NA 8.69E-06 mr1685 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
vg1222921847 NA 3.17E-08 mr1763 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
vg1222921847 NA 8.86E-07 mr1763 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
vg1222921847 NA 3.30E-06 mr1837 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