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Detailed information for vg0629027845:

Variant ID: vg0629027845 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29027845
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGTGAGCTGGTCGAGGTTGAAGTTGCCATGAGGCAGGTTGACGCTGTTCCTGGTCGACACCCTGCCGTCGAACCTGCCGAGCTCCACCGCGTAGTCCGG[T/C]
CCTCCACTCTGCATCATGCAGCCAACCCATCAATGGCCATTCGTGCGTGTTCGAATATAAACTAAATTGCCAGTTTTCTCTTATGAGCTAAAACATTTGA

Reverse complement sequence

TCAAATGTTTTAGCTCATAAGAGAAAACTGGCAATTTAGTTTATATTCGAACACGCACGAATGGCCATTGATGGGTTGGCTGCATGATGCAGAGTGGAGG[A/G]
CCGGACTACGCGGTGGAGCTCGGCAGGTTCGACGGCAGGGTGTCGACCAGGAACAGCGTCAACCTGCCTCATGGCAACTTCAACCTCGACCAGCTCACCG

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 63.30% 36.70% 0.00% 0.00% NA
All Indica  2759 96.30% 3.70% 0.00% 0.00% NA
All Japonica  1512 4.40% 95.60% 0.00% 0.00% NA
Aus  269 45.00% 55.00% 0.00% 0.00% NA
Indica I  595 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.20% 0.00% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 6.50% 93.50% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0629027845 T -> C LOC_Os06g48010.1 synonymous_variant ; p.Gly139Gly; LOW synonymous_codon Average:72.38; most accessible tissue: Zhenshan97 panicle, score: 83.41 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629027845 NA 3.72E-25 mr1251 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
vg0629027845 NA 2.65E-17 mr1253 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
vg0629027845 NA 4.34E-29 mr1638 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
vg0629027845 NA 5.84E-16 mr1968 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
vg0629027845 NA 8.83E-36 mr1129_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
vg0629027845 NA 1.76E-22 mr1253_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
vg0629027845 NA 8.94E-10 mr1349_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