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Detailed information for vg0911580904:

Variant ID: vg0911580904 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 11580904
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCAAACATGTAAATCATTCACAATTAATTTCTAGTAATTCGTATAGTTTAACAACATATGAACTATTCCCTCCGTCCCAAAATAACTCAACCTAGGATG[G/A]
GATGTGACCCATCGTAGGCCAACGAATCTGGACATAGGGAATATGTCACATCTAATACTAGGTTGAGTTATTTTGGCATAGAGGGAGTATATATTAAGAA

Reverse complement sequence

TTCTTAATATATACTCCCTCTATGCCAAAATAACTCAACCTAGTATTAGATGTGACATATTCCCTATGTCCAGATTCGTTGGCCTACGATGGGTCACATC[C/T]
CATCCTAGGTTGAGTTATTTTGGGACGGAGGGAATAGTTCATATGTTGTTAAACTATACGAATTACTAGAAATTAATTGTGAATGATTTACATGTTTGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 3.50% 2.75% 8.38% NA
All Indica  2759 85.20% 4.30% 3.37% 7.10% NA
All Japonica  1512 88.20% 2.90% 0.99% 7.87% NA
Aus  269 67.30% 1.10% 5.95% 25.65% NA
Indica I  595 98.70% 0.30% 0.34% 0.67% NA
Indica II  465 73.50% 8.60% 6.24% 11.61% NA
Indica III  913 83.80% 4.50% 3.50% 8.21% NA
Indica Intermediate  786 83.70% 4.50% 3.82% 8.02% NA
Temperate Japonica  767 83.20% 2.30% 1.43% 13.04% NA
Tropical Japonica  504 92.90% 3.00% 0.79% 3.37% NA
Japonica Intermediate  241 94.60% 4.60% 0.00% 0.83% NA
VI/Aromatic  96 93.80% 0.00% 4.17% 2.08% NA
Intermediate  90 86.70% 0.00% 2.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0911580904 G -> DEL N N silent_mutation Average:29.882; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0911580904 G -> A LOC_Os09g19350.1 intron_variant ; MODIFIER silent_mutation Average:29.882; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0911580904 NA 7.95E-07 mr1137_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
vg0911580904 3.67E-06 3.67E-06 mr1262_2 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
vg0911580904 1.57E-06 4.65E-07 mr1388_2 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
vg0911580904 NA 5.80E-06 mr1482_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
vg0911580904 NA 8.42E-06 mr1554_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
vg0911580904 NA 1.24E-06 mr1609_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
vg0911580904 NA 1.06E-07 mr1617_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
vg0911580904 7.83E-06 2.07E-06 mr1649_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
vg0911580904 NA 3.82E-07 mr1696_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
vg0911580904 NA 7.83E-06 mr1735_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
vg0911580904 NA 8.01E-07 mr1735_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