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Detailed information for vg1004851571:

Variant ID: vg1004851571 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4851571
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACATCTACATGACCATTTGAAAATTTGCACATTGAGAAAGATCAAGATGGGGCCAAAGACACTTGCACAATCTTCATTGAGGTTCAATTCCATAGAGGG[A/G]
GGGAAAGTTTCTGTGGACACATACACATTTGATCCAGCAGTGGCTAGGAGAGAGCTTGCTGCCATGATAATATTACATGAGTATCCTTTATCTATTGTTG

Reverse complement sequence

CAACAATAGATAAAGGATACTCATGTAATATTATCATGGCAGCAAGCTCTCTCCTAGCCACTGCTGGATCAAATGTGTATGTGTCCACAGAAACTTTCCC[T/C]
CCCTCTATGGAATTGAACCTCAATGAAGATTGTGCAAGTGTCTTTGGCCCCATCTTGATCTTTCTCAATGTGCAAATTTTCAAATGGTCATGTAGATGTG

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 40.60% 6.20% 35.48% 17.73% NA
All Indica  2759 9.50% 10.50% 57.27% 22.76% NA
All Japonica  1512 88.20% 0.10% 3.11% 8.60% NA
Aus  269 81.80% 0.40% 3.35% 14.50% NA
Indica I  595 6.10% 6.10% 55.29% 32.61% NA
Indica II  465 12.30% 4.90% 39.14% 43.66% NA
Indica III  913 10.70% 15.40% 67.91% 5.91% NA
Indica Intermediate  786 9.00% 11.30% 57.12% 22.52% NA
Temperate Japonica  767 96.70% 0.00% 1.56% 1.69% NA
Tropical Japonica  504 75.20% 0.20% 5.36% 19.25% NA
Japonica Intermediate  241 88.40% 0.00% 3.32% 8.30% NA
VI/Aromatic  96 60.40% 0.00% 20.83% 18.75% NA
Intermediate  90 48.90% 2.20% 23.33% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004851571 A -> G LOC_Os10g08970.1 synonymous_variant ; p.Gly207Gly; LOW synonymous_codon Average:8.869; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1004851571 A -> DEL LOC_Os10g08970.1 N frameshift_variant Average:8.869; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004851571 NA 7.76E-10 mr1016 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
vg1004851571 NA 3.03E-10 mr1018 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
vg1004851571 NA 1.63E-10 mr1055 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
vg1004851571 NA 1.66E-11 mr1132 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
vg1004851571 7.85E-06 6.99E-15 mr1390 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
vg1004851571 NA 6.11E-15 mr1490 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
vg1004851571 NA 4.43E-07 mr1558_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
vg1004851571 NA 3.66E-14 mr1807_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
vg1004851571 NA 1.55E-06 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