\

Search for Variation information by Variation ID:

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

Detailed information for vg0915671665:

Variant ID: vg0915671665 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 15671665
Reference Allele: GTTAATAAlternative Allele: ATTAATA,G
Primary Allele: GTTAATASecondary Allele: ATTAATA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACGTCCACCCATCCAGCCGCTCTCCTCAGATCCGCAGTACTCCCTCTGTTTCACAATGTAAGTCATTTTAGCATTTCTCACATTCATATTGATGTTAAT[GTTAATA/ATTAATA,G]
AATCTAAATAGATATATATGTCTAGATTCATTAACATCAATATAAATTTGAGAAATACTAGAATGACTTATATTGTTAAACGGAGGGAGTAGCAAATTAA

Reverse complement sequence

TTAATTTGCTACTCCCTCCGTTTAACAATATAAGTCATTCTAGTATTTCTCAAATTTATATTGATGTTAATGAATCTAGACATATATATCTATTTAGATT[TATTAAC/TATTAAT,C]
ATTAACATCAATATGAATGTGAGAAATGCTAAAATGACTTACATTGTGAAACAGAGGGAGTACTGCGGATCTGAGGAGAGCGGCTGGATGGGTGGACGTG

Allele Frequencies:

Populations Population SizeFrequency of GTTAATA(primary allele) Frequency of ATTAATA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.00% 8.90% 1.04% 0.00% G: 0.11%
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 70.20% 26.70% 2.91% 0.00% G: 0.20%
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.50% 0.13% 0.00% NA
Temperate Japonica  767 95.20% 2.70% 2.09% 0.00% NA
Tropical Japonica  504 28.60% 67.70% 3.17% 0.00% G: 0.60%
Japonica Intermediate  241 78.00% 17.00% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 12.20% 3.33% 0.00% G: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0915671665 GTTAATA -> G LOC_Os09g26050-LOC_Os09g26060 intergenic_region ; MODIFIER silent_mutation Average:50.993; most accessible tissue: Zhenshan97 flower, score: 68.734 N N N N
vg0915671665 GTTAATA -> ATTAATA LOC_Os09g26050-LOC_Os09g26060 intergenic_region ; MODIFIER silent_mutation Average:50.993; most accessible tissue: Zhenshan97 flower, score: 68.734 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915671665 NA 2.29E-11 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0915671665 NA 7.85E-09 mr1539 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
vg0915671665 2.21E-06 3.60E-36 mr1699 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
vg0915671665 NA 2.15E-17 mr1699 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
vg0915671665 NA 7.61E-19 mr1715 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
vg0915671665 NA 9.60E-10 mr1379_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
vg0915671665 NA 2.24E-06 mr1422_2 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
vg0915671665 NA 9.71E-12 mr1533_2 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
vg0915671665 NA 6.17E-07 mr1606_2 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
vg0915671665 NA 2.24E-07 mr1696_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
vg0915671665 NA 1.41E-28 mr1699_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
vg0915671665 NA 8.45E-17 mr1715_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
vg0915671665 NA 2.89E-07 mr1819_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
vg0915671665 NA 6.47E-07 mr1873_2 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
vg0915671665 NA 3.27E-10 mr1905_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
vg0915671665 NA 5.97E-07 mr1905_2 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
vg0915671665 NA 4.02E-10 mr1916_2 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
vg0915671665 NA 3.04E-09 mr1942_2 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