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Detailed information for vg0512023102:

Variant ID: vg0512023102 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 12023102
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGCACCAGAATCGAAAAGTACTGTTGCAGGAACTGAGTTAACAAGAAACGTACCCAAAATCACATCTGGAGCATGTTGAGCTTCTGCAGCAGCGACAT[G/A]
ATTTACACGAGCCTTGGATGCTGGTACAGCAGAGTTATTCTGGGCAGGGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGCATAATGTCCTGGA

Reverse complement sequence

TCCAGGACATTATGCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCCCTGCCCAGAATAACTCTGCTGTACCAGCATCCAAGGCTCGTGTAAAT[C/T]
ATGTCGCTGCTGCAGAAGCTCAACATGCTCCAGATGTGATTTTGGGTACGTTTCTTGTTAACTCAGTTCCTGCAACAGTACTTTTCGATTCTGGTGCTAC

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 77.50% 9.10% 5.06% 8.32% NA
All Indica  2759 85.30% 1.00% 5.58% 8.12% NA
All Japonica  1512 72.10% 25.90% 1.79% 0.26% NA
Aus  269 23.40% 0.00% 17.47% 59.11% NA
Indica I  595 91.40% 0.20% 3.36% 5.04% NA
Indica II  465 96.10% 1.50% 1.08% 1.29% NA
Indica III  913 76.60% 0.30% 11.39% 11.72% NA
Indica Intermediate  786 84.40% 2.20% 3.18% 10.31% NA
Temperate Japonica  767 97.40% 1.60% 1.04% 0.00% NA
Tropical Japonica  504 29.00% 67.50% 2.78% 0.79% NA
Japonica Intermediate  241 81.70% 16.20% 2.07% 0.00% NA
VI/Aromatic  96 94.80% 1.00% 3.12% 1.04% NA
Intermediate  90 75.60% 10.00% 8.89% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0512023102 G -> DEL LOC_Os05g20480.1 N frameshift_variant Average:30.487; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0512023102 G -> A LOC_Os05g20480.1 missense_variant ; p.His121Tyr; MODERATE nonsynonymous_codon ; H121Y Average:30.487; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 possibly damaging 1.565 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0512023102 1.09E-06 NA mr1082 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
vg0512023102 NA 1.69E-07 mr1082 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
vg0512023102 NA 2.88E-06 mr1083 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
vg0512023102 NA 1.63E-06 mr1408 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
vg0512023102 NA 1.09E-06 mr1422 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
vg0512023102 NA 8.41E-09 mr1551 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
vg0512023102 NA 1.45E-07 mr1554 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
vg0512023102 NA 2.71E-08 mr1593 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
vg0512023102 NA 1.53E-16 mr1593 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
vg0512023102 NA 7.86E-08 mr1916 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
vg0512023102 NA 9.50E-06 mr1082_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
vg0512023102 NA 1.48E-07 mr1277_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
vg0512023102 NA 8.72E-08 mr1363_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
vg0512023102 NA 4.11E-07 mr1408_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
vg0512023102 NA 1.86E-14 mr1593_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
vg0512023102 NA 4.05E-26 mr1593_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