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Detailed information for vg1221901937:

Variant ID: vg1221901937 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21901937
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGACAGGAGCTGGCGATTGATCTCGGCGGTTCGACCGGTGTTACAACCTCGGTTAGACCGACGATATCCAGGCGGTCAGACCGGCGCTACTACTTCGGT[C/A]
AGACCGTGATCCATCGATTTCGAGGGTAACTTTTATTTCCGCTAAAAGTTTTTGGTTTTTGGGTATACCAACCATTCACCCCCCTCTGGTTGGCTTAGTT

Reverse complement sequence

AACTAAGCCAACCAGAGGGGGGTGAATGGTTGGTATACCCAAAAACCAAAAACTTTTAGCGGAAATAAAAGTTACCCTCGAAATCGATGGATCACGGTCT[G/T]
ACCGAAGTAGTAGCGCCGGTCTGACCGCCTGGATATCGTCGGTCTAACCGAGGTTGTAACACCGGTCGAACCGCCGAGATCAATCGCCAGCTCCTGTCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.30% 11.50% 0.25% 0.00% NA
All Indica  2759 96.60% 3.40% 0.07% 0.00% NA
All Japonica  1512 70.70% 28.60% 0.66% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 88.40% 11.30% 0.34% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 82.40% 16.60% 1.04% 0.00% NA
Tropical Japonica  504 66.90% 33.10% 0.00% 0.00% NA
Japonica Intermediate  241 41.50% 57.70% 0.83% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 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
vg1221901937 C -> A LOC_Os12g35920-LOC_Os12g35930 intergenic_region ; MODIFIER silent_mutation Average:52.596; most accessible tissue: Minghui63 flag leaf, score: 68.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221901937 NA 1.30E-06 mr1057 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
vg1221901937 NA 9.49E-06 mr1057 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
vg1221901937 NA 7.36E-09 mr1057_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
vg1221901937 NA 2.02E-06 mr1057_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
vg1221901937 NA 7.42E-11 mr1691_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
vg1221901937 NA 1.55E-06 mr1691_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