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Detailed information for vg0727091375:

Variant ID: vg0727091375 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27091375
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGACCTCTCACGGTGGCTCCCTCCTCGGAGGTTGAGCAACCGCGACGCCTTACGGTGGCTCCCTCCACGGAGGTTGAGCAACCGTACGTTCCCCTCTTC[C/G]
GCCGACGCTTGCCGAACGACACCGTCCCTGCGGCACGTGACGCCCGATCAGCTGGCACGCCCTTGGTCAGCGCCTCCTCGATCGGCGCTGCCCCGTCGGT

Reverse complement sequence

ACCGACGGGGCAGCGCCGATCGAGGAGGCGCTGACCAAGGGCGTGCCAGCTGATCGGGCGTCACGTGCCGCAGGGACGGTGTCGTTCGGCAAGCGTCGGC[G/C]
GAAGAGGGGAACGTACGGTTGCTCAACCTCCGTGGAGGGAGCCACCGTAAGGCGTCGCGGTTGCTCAACCTCCGAGGAGGGAGCCACCGTGAGAGGTCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 4.30% 0.00% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 94.00% 6.00% 0.00% 0.00% NA
Aus  269 65.10% 34.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 86.70% 13.30% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0727091375 C -> G LOC_Os07g45410.1 missense_variant ; p.Arg1589Gly; MODERATE nonsynonymous_codon ; R1589G Average:58.614; most accessible tissue: Zhenshan97 panicle, score: 76.605 unknown unknown TOLERATED 0.32

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727091375 2.17E-07 2.17E-07 mr1200 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
vg0727091375 NA 1.44E-06 mr1665 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