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

Detailed information for vg0710361771:

Variant ID: vg0710361771 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10361771
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAGACCACTGGTCGAAGATCTTAAACTATTGTGGAAAAAGAAAGGTGTCCCCATGTGGGACGAGGACAAACAAGAGGAGTTTAACCTACTAGCGCTGTT[G/A]
TTCGTAACCATCAACGATTGGCCTGCACTTAGCAACCTTTCCGGTCAGTCCAACAAGGGGTACAAGGCTTGCATTCACTGTATGGATGAAACAGAAAGTA

Reverse complement sequence

TACTTTCTGTTTCATCCATACAGTGAATGCAAGCCTTGTACCCCTTGTTGGACTGACCGGAAAGGTTGCTAAGTGCAGGCCAATCGTTGATGGTTACGAA[C/T]
AACAGCGCTAGTAGGTTAAACTCCTCTTGTTTGTCCTCGTCCCACATGGGGACACCTTTCTTTTTCCACAATAGTTTAAGATCTTCGACCAGTGGTCTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.20% 3.40% 0.55% 0.80% NA
All Indica  2759 96.00% 3.20% 0.83% 0.00% NA
All Japonica  1512 92.70% 4.60% 0.20% 2.51% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.10% 6.70% 2.18% 0.00% NA
Indica II  465 97.40% 1.90% 0.65% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 4.10% 0.89% 0.00% NA
Temperate Japonica  767 91.00% 9.00% 0.00% 0.00% NA
Tropical Japonica  504 91.90% 0.20% 0.60% 7.34% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg0710361771 G -> DEL LOC_Os07g17530.1 N frameshift_variant Average:23.56; most accessible tissue: Minghui63 young leaf, score: 36.684 N N N N
vg0710361771 G -> A LOC_Os07g17530.1 synonymous_variant ; p.Leu259Leu; LOW synonymous_codon Average:23.56; most accessible tissue: Minghui63 young leaf, score: 36.684 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710361771 NA 1.48E-08 mr1028 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
vg0710361771 4.64E-07 9.93E-08 mr1265 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
vg0710361771 7.27E-06 2.05E-06 mr1265 Ind_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
vg0710361771 8.56E-06 2.13E-06 mr1304 Ind_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
vg0710361771 NA 2.35E-06 mr1354 Ind_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
vg0710361771 1.30E-06 1.30E-06 mr1369 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
vg0710361771 NA 2.49E-07 mr1453 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
vg0710361771 2.17E-06 1.45E-06 mr1528 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
vg0710361771 4.03E-06 2.15E-06 mr1528 Ind_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
vg0710361771 NA 8.15E-06 mr1616 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
vg0710361771 NA 1.94E-06 mr1648 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
vg0710361771 NA 7.38E-09 mr1652 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
vg0710361771 NA 2.03E-06 mr1697 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
vg0710361771 NA 2.29E-06 mr1701 Ind_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
vg0710361771 NA 8.59E-06 mr1904 Ind_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
vg0710361771 NA 9.91E-06 mr1702_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