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Detailed information for vg0707041646:

Variant ID: vg0707041646 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 7041646
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTTGCGAGTATAGGGGACAAAACCAAACAATACAGCATAGGACCACACGTCCGCAATTCAAACCCAGAGCAATACCATAATGTTTGCACTGCTAGGA[T/C]
ATGATAGCGTCAACGATTGATTGAGAACACGCACAAGTATCTTCTGTCATGAGGCACATATTCTCTATGCCTGCAATATATTCAATATAAAAATCTAATG

Reverse complement sequence

CATTAGATTTTTATATTGAATATATTGCAGGCATAGAGAATATGTGCCTCATGACAGAAGATACTTGTGCGTGTTCTCAATCAATCGTTGACGCTATCAT[A/G]
TCCTAGCAGTGCAAACATTATGGTATTGCTCTGGGTTTGAATTGCGGACGTGTGGTCCTATGCTGTATTGTTTGGTTTTGTCCCCTATACTCGCAAAATT

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 80.60% 18.30% 1.08% 0.00% NA
All Indica  2759 98.10% 1.80% 0.14% 0.00% NA
All Japonica  1512 44.40% 53.00% 2.65% 0.00% NA
Aus  269 97.40% 0.70% 1.86% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.50% 0.38% 0.00% NA
Temperate Japonica  767 11.20% 84.90% 3.91% 0.00% NA
Tropical Japonica  504 85.50% 13.70% 0.79% 0.00% NA
Japonica Intermediate  241 63.90% 33.60% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 16.70% 2.22% 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
vg0707041646 T -> C LOC_Os07g12370-LOC_Os07g12380 intergenic_region ; MODIFIER silent_mutation Average:29.45; most accessible tissue: Callus, score: 44.476 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707041646 NA 8.24E-10 mr1368 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
vg0707041646 NA 5.11E-08 mr1552 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
vg0707041646 NA 4.51E-07 mr1308_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
vg0707041646 NA 2.99E-07 mr1350_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
vg0707041646 NA 1.41E-20 mr1361_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
vg0707041646 NA 1.21E-09 mr1361_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
vg0707041646 NA 1.65E-06 mr1509_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
vg0707041646 NA 3.42E-09 mr1543_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
vg0707041646 NA 9.10E-06 mr1672_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
vg0707041646 NA 5.27E-12 mr1853_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
vg0707041646 2.14E-08 NA mr1968_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