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Detailed information for vg0721954637:

Variant ID: vg0721954637 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21954637
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATTGTTTGCTAATTTTGATATATCTTGGTGGTTTTTTTGGTACATAGAAAAATTGGTCGGATATTTTTATTAGTTAATTTTGTTTTTTTAGCGTGGAT[G/A]
CAATTGTTCCTTTTTCTCCAAAGTATTGGATTTTATTAGTGTTGTTTATTAATAGTTGGCTTGGCATATAATGGTCTAGACAGAAGGGAGAGTCAGATGG

Reverse complement sequence

CCATCTGACTCTCCCTTCTGTCTAGACCATTATATGCCAAGCCAACTATTAATAAACAACACTAATAAAATCCAATACTTTGGAGAAAAAGGAACAATTG[C/T]
ATCCACGCTAAAAAAACAAAATTAACTAATAAAAATATCCGACCAATTTTTCTATGTACCAAAAAAACCACCAAGATATATCAAAATTAGCAAACAATGA

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 95.40% 2.10% 0.15% 2.35% NA
All Indica  2759 98.40% 0.40% 0.07% 1.09% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 37.20% 32.00% 1.86% 29.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.00% 0.22% NA
Indica III  913 99.60% 0.00% 0.00% 0.44% NA
Indica Intermediate  786 95.30% 1.30% 0.25% 3.18% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 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 94.40% 2.20% 0.00% 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
vg0721954637 G -> DEL N N silent_mutation Average:37.251; most accessible tissue: Callus, score: 51.45 N N N N
vg0721954637 G -> A LOC_Os07g36680.1 intron_variant ; MODIFIER silent_mutation Average:37.251; most accessible tissue: Callus, score: 51.45 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721954637 NA 1.55E-06 mr1415 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
vg0721954637 NA 1.55E-06 mr1567 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
vg0721954637 2.50E-06 NA mr1406_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
vg0721954637 NA 4.48E-18 mr1587_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
vg0721954637 NA 3.86E-06 mr1762_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
vg0721954637 9.02E-07 NA mr1827_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