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Detailed information for vg1001403288:

Variant ID: vg1001403288 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1403288
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGACAACATGAAGTCATCTAGGCATATCAAGAGAAGACTGAAATCTGTCAGAAAGCAGAAAAACTCCGGAGTGATAGCTTTGGACTATATCCAAACG[G/A]
TTAGAAATCTAGCAGATCAGTTTACCAAGGGGCTACCACGTAATGTGATAGACAGTGCATCGAGGGAAATGGGCTTGATACCCACCTAAGGTTGCACAAT

Reverse complement sequence

ATTGTGCAACCTTAGGTGGGTATCAAGCCCATTTCCCTCGATGCACTGTCTATCACATTACGTGGTAGCCCCTTGGTAAACTGATCTGCTAGATTTCTAA[C/T]
CGTTTGGATATAGTCCAAAGCTATCACTCCGGAGTTTTTCTGCTTTCTGACAGATTTCAGTCTTCTCTTGATATGCCTAGATGACTTCATGTTGTCCTTT

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 61.00% 22.00% 10.60% 6.39% NA
All Indica  2759 66.10% 27.40% 5.84% 0.65% NA
All Japonica  1512 65.40% 5.00% 13.89% 15.74% NA
Aus  269 5.90% 70.60% 23.42% 0.00% NA
Indica I  595 59.50% 38.50% 1.85% 0.17% NA
Indica II  465 65.60% 27.50% 5.38% 1.51% NA
Indica III  913 72.10% 19.90% 7.89% 0.11% NA
Indica Intermediate  786 64.60% 27.50% 6.74% 1.15% NA
Temperate Japonica  767 75.90% 0.10% 8.08% 15.91% NA
Tropical Japonica  504 65.10% 13.70% 10.32% 10.91% NA
Japonica Intermediate  241 32.80% 2.10% 39.83% 25.31% NA
VI/Aromatic  96 5.20% 4.20% 56.25% 34.38% NA
Intermediate  90 55.60% 15.60% 14.44% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001403288 G -> A LOC_Os10g03310.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:26.514; most accessible tissue: Callus, score: 40.519 N N N N
vg1001403288 G -> DEL LOC_Os10g03310.1 N splice_donor_variant Average:26.514; most accessible tissue: Callus, score: 40.519 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001403288 2.75E-12 NA mr1486 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
vg1001403288 1.56E-12 1.36E-15 mr1486 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
vg1001403288 2.01E-10 4.84E-22 mr1548 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
vg1001403288 4.98E-10 2.51E-11 mr1548 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
vg1001403288 5.30E-07 NA mr1721 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
vg1001403288 6.35E-07 2.48E-10 mr1721 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
vg1001403288 1.15E-09 NA mr1486_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
vg1001403288 1.42E-11 2.84E-15 mr1486_2 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
vg1001403288 9.42E-09 NA mr1721_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
vg1001403288 1.60E-09 2.24E-12 mr1721_2 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