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Detailed information for vg1200180389:

Variant ID: vg1200180389 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 180389
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGTTCAAAACACAGCCCTTCTTCTAAAGCATATGGTCAAGTTCTATAATGGTGCTGATTTACCATGGGTGAAATTAATCTCACAATCATATTATGAGT[A/C]
TAAAGTTCCACACTTGATGATGAATAAGGGTTCTTTTTGGTGGAGGGACATCACATCTCTTGCAGACATATTCAGGGGGATAGCAAAATGCGAAATCAGG

Reverse complement sequence

CCTGATTTCGCATTTTGCTATCCCCCTGAATATGTCTGCAAGAGATGTGATGTCCCTCCACCAAAAAGAACCCTTATTCATCATCAAGTGTGGAACTTTA[T/G]
ACTCATAATATGATTGTGAGATTAATTTCACCCATGGTAAATCAGCACCATTATAGAACTTGACCATATGCTTTAGAAGAAGGGCTGTGTTTTGAACTCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.40% 0.80% 18.79% 30.98% NA
All Indica  2759 20.20% 1.40% 27.65% 50.71% NA
All Japonica  1512 96.00% 0.10% 1.12% 2.78% NA
Aus  269 62.80% 0.00% 36.06% 1.12% NA
Indica I  595 22.50% 1.50% 28.57% 47.39% NA
Indica II  465 13.10% 2.40% 38.06% 46.45% NA
Indica III  913 20.50% 1.00% 22.23% 56.30% NA
Indica Intermediate  786 22.40% 1.30% 27.10% 49.24% NA
Temperate Japonica  767 94.50% 0.00% 1.83% 3.65% NA
Tropical Japonica  504 97.40% 0.00% 0.20% 2.38% NA
Japonica Intermediate  241 97.90% 0.40% 0.83% 0.83% NA
VI/Aromatic  96 94.80% 0.00% 3.12% 2.08% NA
Intermediate  90 71.10% 0.00% 8.89% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1200180389 A -> C LOC_Os12g01320.1 missense_variant ; p.Tyr284Ser; MODERATE nonsynonymous_codon ; Y284S Average:16.865; most accessible tissue: Zhenshan97 root, score: 39.742 unknown unknown TOLERATED 0.61
vg1200180389 A -> DEL LOC_Os12g01320.1 N frameshift_variant Average:16.865; most accessible tissue: Zhenshan97 root, score: 39.742 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200180389 NA 6.32E-20 mr1021 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
vg1200180389 NA 4.15E-06 mr1029 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
vg1200180389 NA 7.99E-09 mr1047 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
vg1200180389 NA 5.13E-16 mr1165 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
vg1200180389 NA 2.55E-06 mr1189 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
vg1200180389 NA 4.20E-06 mr1216 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
vg1200180389 NA 1.17E-15 mr1323 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
vg1200180389 NA 1.50E-11 mr1325 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
vg1200180389 NA 1.58E-13 mr1326 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
vg1200180389 NA 8.78E-06 mr1336 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
vg1200180389 NA 1.11E-20 mr1477 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
vg1200180389 NA 6.12E-14 mr1478 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
vg1200180389 NA 1.57E-06 mr1532 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
vg1200180389 NA 4.43E-13 mr1744 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
vg1200180389 NA 6.94E-08 mr1781 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
vg1200180389 NA 5.89E-07 mr1796 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
vg1200180389 4.80E-06 NA mr1808 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
vg1200180389 NA 1.21E-06 mr1850 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
vg1200180389 NA 9.54E-07 mr1990 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
vg1200180389 NA 5.87E-28 mr1270_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
vg1200180389 8.33E-06 9.51E-27 mr1316_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
vg1200180389 NA 1.15E-06 mr1727_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