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Detailed information for vg0627986717:

Variant ID: vg0627986717 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27986717
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCAAGATGTTTCACAAATGGGGTTCGCCAGTCATATGGGTCTTCGCCCAGTTTCTCCTGATCGATTGCCATGACTTCGGAGCAGTCCATTGGCACACTC[A/G]
GAGCATGCAGGACTTCGCAAAAGATGCCCGGCGAATGCGGGCCACCACAAGCAGCGGATTTCGCCAAGGCGTCTGCTTCCCCGTTCTGGTCTCTAGGCAA

Reverse complement sequence

TTGCCTAGAGACCAGAACGGGGAAGCAGACGCCTTGGCGAAATCCGCTGCTTGTGGTGGCCCGCATTCGCCGGGCATCTTTTGCGAAGTCCTGCATGCTC[T/C]
GAGTGTGCCAATGGACTGCTCCGAAGTCATGGCAATCGATCAGGAGAAACTGGGCGAAGACCCATATGACTGGCGAACCCCATTTGTGAAACATCTTGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 3.60% 0.42% 1.71% NA
All Indica  2759 99.50% 0.30% 0.22% 0.00% NA
All Japonica  1512 86.70% 10.10% 0.13% 3.04% NA
Aus  269 96.30% 3.00% 0.37% 0.37% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.20% 0.66% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 80.80% 19.20% 0.00% 0.00% NA
Tropical Japonica  504 91.10% 0.80% 0.40% 7.74% NA
Japonica Intermediate  241 96.30% 0.80% 0.00% 2.90% NA
VI/Aromatic  96 56.20% 0.00% 8.33% 35.42% NA
Intermediate  90 93.30% 3.30% 3.33% 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
vg0627986717 A -> G LOC_Os06g46180.1 missense_variant ; p.Leu1385Pro; MODERATE nonsynonymous_codon ; L1385P Average:31.06; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 possibly damaging -1.668 TOLERATED 1.00
vg0627986717 A -> DEL LOC_Os06g46180.1 N frameshift_variant Average:31.06; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627986717 NA 2.84E-08 Awn_length Jap_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
vg0627986717 NA 4.41E-06 mr1057 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
vg0627986717 NA 1.79E-06 mr1062 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
vg0627986717 1.91E-07 NA mr1210 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
vg0627986717 NA 5.26E-07 mr1210 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
vg0627986717 3.12E-07 NA mr1305 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
vg0627986717 NA 3.43E-06 mr1305 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
vg0627986717 NA 2.78E-07 mr1585 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
vg0627986717 1.12E-09 NA mr1586 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
vg0627986717 NA 7.11E-08 mr1586 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
vg0627986717 NA 1.06E-08 mr1624 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
vg0627986717 NA 1.82E-06 mr1765 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
vg0627986717 NA 1.15E-07 mr1057_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
vg0627986717 5.65E-06 5.65E-06 mr1166_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
vg0627986717 3.68E-08 NA mr1305_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
vg0627986717 NA 9.20E-08 mr1305_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
vg0627986717 NA 1.28E-07 mr1585_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
vg0627986717 NA 8.29E-09 mr1585_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
vg0627986717 1.75E-06 NA mr1765_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
vg0627986717 NA 4.00E-07 mr1765_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