Search for Variation information by Variation ID:

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

Detailed information for vg0507887261:

Variant ID: vg0507887261 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7887261
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CACAGCCGAGTACGAGGGACTACTCGCCGGGATAAGAGCTACAGTTGCACTTGGAGTCAAGCGACTGATCGTGAAAGGGGATTCCGAACTAGTCGCAAAC[C/T]
AGGTGCACAAAGATTACAAATGCTCTAGCCCAAAGCTGTCTAATTATCTCGCAGAAGTCAGGAAGCTGGAAAAAAGATTTGATGGGATCGAGGTCCGACA

Reverse complement sequence

TGTCGGACCTCGATCCCATCAAATCTTTTTTCCAGCTTCCTGACTTCTGCGAGATAATTAGACAGCTTTGGGCTAGAGCATTTGTAATCTTTGTGCACCT[G/A]
GTTTGCGACTAGTTCGGAATCCCCTTTCACGATCAGTCGCTTGACTCCAAGTGCAACTGTAGCTCTTATCCCGGCGAGTAGTCCCTCGTACTCGGCTGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.50% 46.00% 0.02% 0.42% NA
All Indica  2759 24.40% 75.00% 0.04% 0.58% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 7.10% 92.10% 0.00% 0.84% NA
Indica II  465 32.30% 67.30% 0.00% 0.43% NA
Indica III  913 27.20% 72.40% 0.00% 0.44% NA
Indica Intermediate  786 29.80% 69.50% 0.13% 0.64% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 63.30% 32.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0507887261 C -> T LOC_Os05g14110.1 stop_gained ; p.Gln1210*; HIGH stop_gained Average:47.915; most accessible tissue: Minghui63 flag leaf, score: 75.722 N N N N
vg0507887261 C -> DEL LOC_Os05g14110.1 N frameshift_variant Average:47.915; most accessible tissue: Minghui63 flag leaf, score: 75.722 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507887261 NA 1.75E-09 mr1191 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
vg0507887261 NA 5.33E-06 mr1632 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
vg0507887261 3.03E-07 1.19E-27 mr1039_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
vg0507887261 NA 4.13E-15 mr1514_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
vg0507887261 1.45E-10 1.64E-31 mr1632_2 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
vg0507887261 6.19E-09 4.46E-08 mr1632_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
vg0507887261 NA 6.35E-06 mr1873_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