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Detailed information for vg1215271479:

Variant ID: vg1215271479 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15271479
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTCAAACAACCACCAGGTTTTGAAAATCCTGATTTTCCCAACCATGTTTTTAAATTGTCTAAAGCTTTATATGGTTTGAAACAAGCTCCCAGGGCATGG[T/C]
ATGATAGGCTTAAGAACTTTTTGCTTGCAAAAGGTTTTTACAATGGGAAAGGTTGACAAAACGCTTTTTGTTTCTTAAGCATGGTGATAATCAACTTTTC

Reverse complement sequence

GAAAAGTTGATTATCACCATGCTTAAGAAACAAAAAGCGTTTTGTCAACCTTTCCCATTGTAAAAACCTTTTGCAAGCAAAAAGTTCTTAAGCCTATCAT[A/G]
CCATGCCCTGGGAGCTTGTTTCAAACCATATAAAGCTTTAGACAATTTAAAAACATGGTTGGGAAAATCAGGATTTTCAAAACCTGGTGGTTGTTTGACA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.50% 7.10% 3.09% 8.32% NA
All Indica  2759 84.80% 0.60% 3.41% 11.16% NA
All Japonica  1512 73.00% 18.90% 3.04% 5.03% NA
Aus  269 92.20% 6.30% 0.00% 1.49% NA
Indica I  595 96.80% 0.00% 2.35% 0.84% NA
Indica II  465 82.80% 0.40% 2.58% 14.19% NA
Indica III  913 78.90% 0.30% 3.40% 17.42% NA
Indica Intermediate  786 84.00% 1.40% 4.71% 9.92% NA
Temperate Japonica  767 86.70% 8.00% 3.91% 1.43% NA
Tropical Japonica  504 56.20% 31.70% 0.99% 11.11% NA
Japonica Intermediate  241 64.70% 27.00% 4.56% 3.73% NA
VI/Aromatic  96 91.70% 6.20% 2.08% 0.00% NA
Intermediate  90 76.70% 13.30% 4.44% 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
vg1215271479 T -> C LOC_Os12g26190.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:7.847; most accessible tissue: Callus, score: 12.192 N N N N
vg1215271479 T -> DEL LOC_Os12g26190.1 N splice_donor_variant Average:7.847; most accessible tissue: Callus, score: 12.192 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215271479 6.13E-07 NA mr1018 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
vg1215271479 2.67E-06 NA mr1019 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
vg1215271479 1.24E-07 NA mr1055 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
vg1215271479 7.58E-07 NA mr1142 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
vg1215271479 1.33E-07 NA mr1489 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
vg1215271479 7.84E-06 NA mr1491 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
vg1215271479 2.09E-07 NA mr1778 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
vg1215271479 7.69E-10 NA mr1019_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
vg1215271479 2.36E-08 NA mr1023_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
vg1215271479 3.58E-07 NA mr1055_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
vg1215271479 NA 8.39E-06 mr1072_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
vg1215271479 NA 6.82E-07 mr1077_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
vg1215271479 NA 8.76E-06 mr1100_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
vg1215271479 3.41E-06 NA mr1132_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
vg1215271479 1.51E-08 NA mr1489_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
vg1215271479 6.61E-07 NA mr1778_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