\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0328202089:

Variant ID: vg0328202089 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28202089
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAGTACCTGTGGGGGGCACAACAGAAGGCCTAGCCGAGGAAGGCGGGGTGCTGAACGGTGCACGAAACCCTGAAGCAATCGGCAAGTGAAACGGCTCAC[A/T]
TATATGTGCGAGGCATGTGCAGAAAAATCCTTAAAAATACTTACCTCCGTGCGGAGGGGGAGTCGGCCTAGGAACGTGCGCAGCTGGACGGGGACCAGTC

Reverse complement sequence

GACTGGTCCCCGTCCAGCTGCGCACGTTCCTAGGCCGACTCCCCCTCCGCACGGAGGTAAGTATTTTTAAGGATTTTTCTGCACATGCCTCGCACATATA[T/A]
GTGAGCCGTTTCACTTGCCGATTGCTTCAGGGTTTCGTGCACCGTTCAGCACCCCGCCTTCCTCGGCTAGGCCTTCTGTTGTGCCCCCCACAGGTACTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 6.00% 7.34% 0.00% NA
All Indica  2759 86.80% 3.30% 9.89% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 13.80% 61.00% 25.28% 0.00% NA
Indica I  595 58.00% 5.70% 36.30% 0.00% NA
Indica II  465 92.50% 3.40% 4.09% 0.00% NA
Indica III  913 97.00% 2.50% 0.44% 0.00% NA
Indica Intermediate  786 93.50% 2.20% 4.33% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 19.80% 1.04% 0.00% NA
Intermediate  90 84.40% 11.10% 4.44% 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
vg0328202089 A -> T LOC_Os03g49530.1 intron_variant ; MODIFIER silent_mutation Average:17.617; most accessible tissue: Minghui63 root, score: 29.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328202089 NA 2.33E-06 mr1006 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
vg0328202089 NA 1.71E-08 mr1038 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
vg0328202089 NA 5.02E-07 mr1038 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
vg0328202089 NA 4.53E-06 mr1052 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
vg0328202089 NA 6.22E-10 mr1389 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
vg0328202089 NA 1.10E-07 mr1389 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
vg0328202089 NA 9.03E-06 mr1433 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
vg0328202089 NA 3.09E-06 mr1621 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
vg0328202089 1.64E-06 1.63E-06 mr1753 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
vg0328202089 NA 5.59E-07 mr1764 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
vg0328202089 NA 3.43E-07 mr1810 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
vg0328202089 NA 1.80E-06 mr1931 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
vg0328202089 NA 9.05E-06 mr1948 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
vg0328202089 NA 1.61E-06 mr1038_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
vg0328202089 NA 2.21E-06 mr1389_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
vg0328202089 NA 3.70E-06 mr1389_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