Search for Variation information by Variation ID:

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

Detailed information for vg0906051911:

Variant ID: vg0906051911 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6051911
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGAGGAGGAAGGAGGATAAGGGATAGGATTATATACTACACTTCGAATTTTAGTTCCAATTGATCTTTAGTCCCGGTTTGGAACACCAACCGGAACTAA[T/C]
AACCGGGACTAAAGATCATATTTAATCCGGGTTGGGAACACCAACCGGAACTAAAGTGGTGACACCAACCGGGACTAAAGATTCTCGGCCCCCTGACATC

Reverse complement sequence

GATGTCAGGGGGCCGAGAATCTTTAGTCCCGGTTGGTGTCACCACTTTAGTTCCGGTTGGTGTTCCCAACCCGGATTAAATATGATCTTTAGTCCCGGTT[A/G]
TTAGTTCCGGTTGGTGTTCCAAACCGGGACTAAAGATCAATTGGAACTAAAATTCGAAGTGTAGTATATAATCCTATCCCTTATCCTCCTTCCTCCTCCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.30% 24.50% 0.23% 0.00% NA
All Indica  2759 68.80% 30.90% 0.33% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 82.40% 17.10% 0.50% 0.00% NA
Indica II  465 46.90% 53.10% 0.00% 0.00% NA
Indica III  913 74.70% 25.10% 0.22% 0.00% NA
Indica Intermediate  786 64.50% 35.00% 0.51% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 72.20% 25.60% 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
vg0906051911 T -> C LOC_Os09g10960.1 upstream_gene_variant ; 2635.0bp to feature; MODIFIER silent_mutation Average:74.926; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg0906051911 T -> C LOC_Os09g10960-LOC_Os09g10970 intergenic_region ; MODIFIER silent_mutation Average:74.926; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906051911 NA 7.60E-10 mr1498 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
vg0906051911 3.89E-06 4.88E-06 mr1570 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
vg0906051911 NA 5.94E-06 mr1657 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
vg0906051911 NA 5.57E-08 mr1705 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
vg0906051911 NA 7.95E-08 mr1951 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