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Detailed information for vg1010611588:

Variant ID: vg1010611588 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10611588
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCATAGGCATGCTAAATGGGTTGAATTTATTGAATCTTTTCCATATGTCATCAAACATAAGAAGGGAAAAGAAAATGTCATTGCTGATGCTTTGTCTA[G/A]
ACGTTACACAATGCTATCCCAACTTGACTTCAAAATTTTTGGCTTGGAAACAATAAAAGAGCAATATGCGCACGATGATGATTTTAAAGATGTGTTGTTG

Reverse complement sequence

CAACAACACATCTTTAAAATCATCATCGTGCGCATATTGCTCTTTTATTGTTTCCAAGCCAAAAATTTTGAAGTCAAGTTGGGATAGCATTGTGTAACGT[C/T]
TAGACAAAGCATCAGCAATGACATTTTCTTTTCCCTTCTTATGTTTGATGACATATGGAAAAGATTCAATAAATTCAACCCATTTAGCATGCCTATGGTT

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 96.60% 1.40% 0.61% 1.38% NA
All Indica  2759 99.90% 0.00% 0.04% 0.04% NA
All Japonica  1512 89.70% 4.30% 1.79% 4.17% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 88.70% 8.20% 1.96% 1.17% NA
Tropical Japonica  504 96.80% 0.20% 0.99% 1.98% NA
Japonica Intermediate  241 78.40% 0.40% 2.90% 18.26% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1010611588 G -> A LOC_Os10g20960.1 missense_variant ; p.Arg1005Lys; MODERATE nonsynonymous_codon ; R1005K Average:19.926; most accessible tissue: Minghui63 young leaf, score: 31.294 benign 1.278 TOLERATED 0.06
vg1010611588 G -> DEL LOC_Os10g20960.1 N frameshift_variant Average:19.926; most accessible tissue: Minghui63 young leaf, score: 31.294 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010611588 3.10E-06 3.10E-06 mr1956 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
vg1010611588 NA 1.78E-06 mr1693_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