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Detailed information for vg1200149931:

Variant ID: vg1200149931 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 149931
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACCTGGCACCAGATCCTTTTTTCTCCCATTCTGAATCCAAGTAAATTTCATAAAACTACAGGTATTTTGCACAATTTATCACAAAACTACATATTTAA[G/A]
AGCTTGTTTCACAAAACTACAGATTTAATGTCTCTGTTTATCACAAAACTACAGGTACTTTGTATAATCTATCATAAAACTATATATTTAAGAACTTGTT

Reverse complement sequence

AACAAGTTCTTAAATATATAGTTTTATGATAGATTATACAAAGTACCTGTAGTTTTGTGATAAACAGAGACATTAAATCTGTAGTTTTGTGAAACAAGCT[C/T]
TTAAATATGTAGTTTTGTGATAAATTGTGCAAAATACCTGTAGTTTTATGAAATTTACTTGGATTCAGAATGGGAGAAAAAAGGATCTGGTGCCAGGTCT

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 92.60% 6.70% 0.11% 0.61% NA
All Indica  2759 89.70% 9.20% 0.07% 1.01% NA
All Japonica  1512 96.00% 3.80% 0.20% 0.00% NA
Aus  269 98.50% 1.10% 0.00% 0.37% NA
Indica I  595 77.80% 21.70% 0.00% 0.50% NA
Indica II  465 99.60% 0.20% 0.00% 0.22% NA
Indica III  913 93.20% 5.10% 0.00% 1.64% NA
Indica Intermediate  786 88.90% 9.70% 0.25% 1.15% NA
Temperate Japonica  767 92.20% 7.40% 0.39% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg1200149931 G -> DEL N N silent_mutation Average:30.243; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg1200149931 G -> A LOC_Os12g01250.1 intron_variant ; MODIFIER silent_mutation Average:30.243; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200149931 2.29E-06 NA mr1300 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
vg1200149931 3.38E-08 NA mr1310 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
vg1200149931 NA 1.19E-06 mr1310 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
vg1200149931 1.07E-08 NA mr1926 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
vg1200149931 NA 1.38E-07 mr1926 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
vg1200149931 4.78E-06 NA mr1959 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