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Detailed information for vg0701261601:

Variant ID: vg0701261601 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 1261601
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, G: 0.42, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCGCTGGTGGCTCGTTTTATCTAACAGCCAGCGAAAATCTATTTTTGCTGGCGGTCCGTAGCCTCCCACCCCTCGTTATGTTTTTGCTGGCGGTTTTT[A/G]
CGTATAGCCGCCAAAGAAAATAATAGGGTGACGCCATGAAATATCTTTTTTCTAGTAGTGACACACATATTCAAATTCGTAGTATTAGGATATATCACTG

Reverse complement sequence

CAGTGATATATCCTAATACTACGAATTTGAATATGTGTGTCACTACTAGAAAAAAGATATTTCATGGCGTCACCCTATTATTTTCTTTGGCGGCTATACG[T/C]
AAAAACCGCCAGCAAAAACATAACGAGGGGTGGGAGGCTACGGACCGCCAGCAAAAATAGATTTTCGCTGGCTGTTAGATAAAACGAGCCACCAGCGAAA

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 87.50% 10.00% 0.40% 2.07% NA
All Indica  2759 94.80% 1.10% 0.62% 3.52% NA
All Japonica  1512 80.00% 19.90% 0.07% 0.00% NA
Aus  269 80.70% 19.00% 0.37% 0.00% NA
Indica I  595 96.80% 2.90% 0.34% 0.00% NA
Indica II  465 88.60% 0.20% 0.86% 10.32% NA
Indica III  913 96.90% 0.50% 0.55% 1.97% NA
Indica Intermediate  786 94.40% 0.90% 0.76% 3.94% NA
Temperate Japonica  767 68.70% 31.30% 0.00% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.30% 0.41% 0.00% NA
VI/Aromatic  96 18.80% 81.20% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0701261601 A -> DEL N N silent_mutation Average:64.627; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg0701261601 A -> G LOC_Os07g03210.1 intron_variant ; MODIFIER silent_mutation Average:64.627; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0701261601 1.23E-07 8.20E-29 Awn_length 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
vg0701261601 NA 1.34E-09 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
vg0701261601 2.53E-06 NA mr1379 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
vg0701261601 NA 1.23E-06 mr1707 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
vg0701261601 NA 9.55E-08 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