\

Search for Variation information by Variation ID:

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

Detailed information for vg0712408577:

Variant ID: vg0712408577 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12408577
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGAACAACCTTGCAAGAACTGACCTTGTAAACCATAACCACTATAGGTAGCACTTGTTGCCTCTGGGATTGGGGGTGACTTAGCTGTGCTGGTCTGCT[A/G]
AAGACTTGGTGGCGTACTGTCTGAGGTTGCAGGTGCTTGCTCTTGGAAAACAAACTGACTTTCGCTCTGATCCTGATTCCGGCTTGCATCTGAGCTTGTA

Reverse complement sequence

TACAAGCTCAGATGCAAGCCGGAATCAGGATCAGAGCGAAAGTCAGTTTGTTTTCCAAGAGCAAGCACCTGCAACCTCAGACAGTACGCCACCAAGTCTT[T/C]
AGCAGACCAGCACAGCTAAGTCACCCCCAATCCCAGAGGCAACAAGTGCTACCTATAGTGGTTATGGTTTACAAGGTCAGTTCTTGCAAGGTTGTTCAAC

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 26.40% 8.70% 19.32% 45.58% NA
All Indica  2759 2.30% 9.60% 18.88% 69.19% NA
All Japonica  1512 75.50% 7.50% 7.14% 9.85% NA
Aus  269 1.90% 9.70% 61.71% 26.77% NA
Indica I  595 2.00% 6.20% 17.14% 74.62% NA
Indica II  465 3.90% 7.30% 16.34% 72.47% NA
Indica III  913 1.80% 12.70% 14.13% 71.41% NA
Indica Intermediate  786 2.30% 9.90% 27.23% 60.56% NA
Temperate Japonica  767 67.50% 10.30% 5.74% 16.43% NA
Tropical Japonica  504 86.10% 3.40% 9.92% 0.60% NA
Japonica Intermediate  241 78.80% 7.10% 5.81% 8.30% NA
VI/Aromatic  96 0.00% 4.20% 95.83% 0.00% NA
Intermediate  90 38.90% 5.60% 28.89% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0712408577 A -> DEL N N silent_mutation Average:39.551; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0712408577 A -> G LOC_Os07g22210-LOC_Os07g22220 intergenic_region ; MODIFIER silent_mutation Average:39.551; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712408577 NA 3.72E-20 mr1676 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
vg0712408577 NA 1.30E-13 mr1900 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
vg0712408577 NA 9.82E-10 mr1905 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
vg0712408577 2.02E-06 1.46E-25 mr1042_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
vg0712408577 NA 1.71E-20 mr1167_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
vg0712408577 NA 7.84E-07 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
vg0712408577 NA 1.17E-06 mr1418_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
vg0712408577 NA 1.98E-07 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
vg0712408577 NA 4.63E-07 mr1479_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
vg0712408577 NA 5.14E-06 mr1574_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
vg0712408577 NA 6.85E-13 mr1636_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
vg0712408577 NA 1.22E-12 mr1641_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
vg0712408577 NA 2.55E-11 mr1646_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
vg0712408577 NA 9.39E-11 mr1667_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
vg0712408577 NA 1.80E-09 mr1681_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
vg0712408577 NA 9.88E-08 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
vg0712408577 NA 2.91E-17 mr1726_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
vg0712408577 NA 2.89E-13 mr1838_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
vg0712408577 NA 4.84E-14 mr1950_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
vg0712408577 NA 8.61E-11 mr1986_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