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Detailed information for vg0601102379:

Variant ID: vg0601102379 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1102379
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCTCTTAACTGATGTGCGGCGTAAAGGGTTTTCTCTTGCGGAGTACACTGTACCAGATTTAATTTCCTTTCCATATCTTTAATCCAATCATCAGCTTC[A/G]
ATAGGCTCATTTGTTTGGGAGAACTCCGGTGGACGAGATCCCAAGAAATCATTCAGTTTCGATTGGCCATCATCTTGAACCATATGGGGTTGACGCTCTT

Reverse complement sequence

AAGAGCGTCAACCCCATATGGTTCAAGATGATGGCCAATCGAAACTGAATGATTTCTTGGGATCTCGTCCACCGGAGTTCTCCCAAACAAATGAGCCTAT[T/C]
GAAGCTGATGATTGGATTAAAGATATGGAAAGGAAATTAAATCTGGTACAGTGTACTCCGCAAGAGAAAACCCTTTACGCCGCACATCAGTTAAGAGGAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 2.00% 0.97% 8.13% NA
All Indica  2759 88.10% 3.30% 1.52% 7.03% NA
All Japonica  1512 98.70% 0.00% 0.07% 1.19% NA
Aus  269 38.30% 0.00% 1.12% 60.59% NA
Indica I  595 92.40% 0.30% 0.00% 7.23% NA
Indica II  465 91.60% 7.30% 0.22% 0.86% NA
Indica III  913 83.10% 1.90% 3.72% 11.28% NA
Indica Intermediate  786 88.70% 4.80% 0.89% 5.60% NA
Temperate Japonica  767 99.20% 0.00% 0.13% 0.65% NA
Tropical Japonica  504 97.60% 0.00% 0.00% 2.38% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 93.80% 0.00% 0.00% 6.25% 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
vg0601102379 A -> G LOC_Os06g03000.1 synonymous_variant ; p.Ile124Ile; LOW synonymous_codon Average:28.322; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg0601102379 A -> DEL LOC_Os06g03000.1 N frameshift_variant Average:28.322; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601102379 NA 6.60E-08 mr1310 Ind_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
vg0601102379 1.71E-06 1.71E-06 mr1926 Ind_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
vg0601102379 NA 4.20E-06 mr1449_2 Ind_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
vg0601102379 NA 6.18E-08 mr1712_2 Ind_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
vg0601102379 5.64E-06 1.88E-07 mr1717_2 Ind_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
vg0601102379 NA 2.26E-06 mr1733_2 Ind_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