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Detailed information for vg0604550200:

Variant ID: vg0604550200 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4550200
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGTCGGGCCCGAGGGTGACGTGGCCACCCCTCCCTCTGTCTCCCCGAGGGGTCGGGCCGCTCCCGTTTCGGCCCCGAGGCCTGGGACGCCCCGACCCC[C/T]
TATGGTTTTGGCGCCACGTGTGTGGGATAGGTGAGCCCAGCGGGGCTCACCTAACCGCATTTATAGCGGATTGGACGAGCGCGCCACGCCGCATTTAATG

Reverse complement sequence

CATTAAATGCGGCGTGGCGCGCTCGTCCAATCCGCTATAAATGCGGTTAGGTGAGCCCCGCTGGGCTCACCTATCCCACACACGTGGCGCCAAAACCATA[G/A]
GGGGTCGGGGCGTCCCAGGCCTCGGGGCCGAAACGGGAGCGGCCCGACCCCTCGGGGAGACAGAGGGAGGGGTGGCCACGTCACCCTCGGGCCCGACCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.00% 8.20% 1.82% 0.00% NA
All Indica  2759 96.60% 0.70% 2.72% 0.00% NA
All Japonica  1512 75.80% 23.60% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 83.00% 2.40% 14.62% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 0.60% 0.89% 0.00% NA
Temperate Japonica  767 81.00% 18.90% 0.13% 0.00% NA
Tropical Japonica  504 69.20% 29.60% 1.19% 0.00% NA
Japonica Intermediate  241 73.00% 26.10% 0.83% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0604550200 C -> T LOC_Os06g09030.1 upstream_gene_variant ; 3011.0bp to feature; MODIFIER silent_mutation Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg0604550200 C -> T LOC_Os06g09040.1 downstream_gene_variant ; 1677.0bp to feature; MODIFIER silent_mutation Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg0604550200 C -> T LOC_Os06g09030-LOC_Os06g09040 intergenic_region ; MODIFIER silent_mutation Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604550200 NA 1.52E-06 mr1636 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
vg0604550200 NA 2.54E-06 mr1766 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
vg0604550200 1.29E-09 NA mr1137_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
vg0604550200 3.89E-07 NA mr1137_2 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