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

Detailed information for vg0727263961:

Variant ID: vg0727263961 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27263961
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCGGAGGCGGATTGAATGCGTTGTATGGTACAACTGGCAGTTGATGTGAGTAGCTGACGACAATAGCGTTCGAGAATATCTTGTACATCCTCTCCTTCA[G/T]
GATCTTAAAATCCAAAGAATCTGGGTCTTCACGGTTTGGATCATGCTTGCCGTCAAACTCAAATGCTGTGCGGGATCTTTCTTTGATTGGAGCTAATCGG

Reverse complement sequence

CCGATTAGCTCCAATCAAAGAAAGATCCCGCACAGCATTTGAGTTTGACGGCAAGCATGATCCAAACCGTGAAGACCCAGATTCTTTGGATTTTAAGATC[C/A]
TGAAGGAGAGGATGTACAAGATATTCTCGAACGCTATTGTCGTCAGCTACTCACATCAACTGCCAGTTGTACCATACAACGCATTCAATCCGCCTCCGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.00% 0.60% 45.81% 7.58% NA
All Indica  2759 23.50% 0.20% 65.64% 10.69% NA
All Japonica  1512 93.80% 0.00% 3.70% 2.51% NA
Aus  269 12.30% 7.40% 75.09% 5.20% NA
Indica I  595 35.80% 0.00% 44.03% 20.17% NA
Indica II  465 26.70% 0.00% 63.87% 9.46% NA
Indica III  913 4.80% 0.30% 88.94% 5.91% NA
Indica Intermediate  786 33.80% 0.40% 55.98% 9.80% NA
Temperate Japonica  767 96.50% 0.00% 1.69% 1.83% NA
Tropical Japonica  504 88.50% 0.00% 7.34% 4.17% NA
Japonica Intermediate  241 96.30% 0.00% 2.49% 1.24% NA
VI/Aromatic  96 19.80% 0.00% 73.96% 6.25% NA
Intermediate  90 65.60% 1.10% 27.78% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0727263961 G -> DEL LOC_Os07g45660.1 N frameshift_variant Average:9.878; most accessible tissue: Callus, score: 24.63 N N N N
vg0727263961 G -> T LOC_Os07g45660.1 missense_variant ; p.Leu262Met; MODERATE nonsynonymous_codon ; L262M Average:9.878; most accessible tissue: Callus, score: 24.63 benign 0.341 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727263961 NA 2.97E-06 mr1028 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
vg0727263961 NA 3.07E-08 mr1245 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
vg0727263961 3.10E-07 NA mr1301 Jap_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
vg0727263961 NA 2.73E-09 mr1336 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
vg0727263961 NA 2.69E-07 mr1850 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
vg0727263961 NA 3.51E-19 mr1336_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
vg0727263961 NA 6.26E-08 mr1369_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
vg0727263961 NA 5.07E-08 mr1453_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
vg0727263961 NA 2.58E-16 mr1579_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
vg0727263961 NA 9.77E-21 mr1682_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
vg0727263961 NA 2.21E-07 mr1683_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
vg0727263961 NA 4.35E-08 mr1690_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