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Detailed information for vg1221512382:

Variant ID: vg1221512382 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21512382
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCACTATTTTGAAGGACCACATCGATCTGGTCCCTCAAGAAGAAAAAGAAGAGGCCTGGAGGCAGTTCAAGGAAAGCTTCCAATACCCTACAGAGGCCGA[C/G]
GCAGGACTCAAGCGGCAGGCTATCCGCAAGATGGGAAATTGTTGGAAAAATTTCAAGACAACGCTGGTCACGGAGTACGTCCTCAACCCCGCCCAGCCAG

Reverse complement sequence

CTGGCTGGGCGGGGTTGAGGACGTACTCCGTGACCAGCGTTGTCTTGAAATTTTTCCAACAATTTCCCATCTTGCGGATAGCCTGCCGCTTGAGTCCTGC[G/C]
TCGGCCTCTGTAGGGTATTGGAAGCTTTCCTTGAACTGCCTCCAGGCCTCTTCTTTTTCTTCTTGAGGGACCAGATCGATGTGGTCCTTCAAAATAGTGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.30% 16.60% 6.05% 0.00% NA
All Indica  2759 87.20% 6.80% 6.02% 0.00% NA
All Japonica  1512 54.00% 38.60% 7.34% 0.00% NA
Aus  269 98.50% 0.00% 1.49% 0.00% NA
Indica I  595 70.10% 16.00% 13.95% 0.00% NA
Indica II  465 86.00% 6.70% 7.31% 0.00% NA
Indica III  913 99.10% 0.50% 0.33% 0.00% NA
Indica Intermediate  786 87.00% 7.10% 5.85% 0.00% NA
Temperate Japonica  767 25.90% 65.10% 9.00% 0.00% NA
Tropical Japonica  504 88.10% 8.50% 3.37% 0.00% NA
Japonica Intermediate  241 72.20% 17.40% 10.37% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 16.70% 5.56% 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
vg1221512382 C -> G LOC_Os12g35380.1 missense_variant ; p.Asp98Glu; MODERATE nonsynonymous_codon ; D98E Average:50.527; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221512382 3.24E-07 NA mr1670 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
vg1221512382 NA 9.40E-06 mr1057_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
vg1221512382 NA 5.42E-06 mr1182_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
vg1221512382 NA 8.92E-07 mr1227_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
vg1221512382 NA 1.18E-07 mr1308_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
vg1221512382 NA 4.52E-06 mr1575_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
vg1221512382 NA 3.74E-10 mr1584_2 Jap_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
vg1221512382 1.24E-07 NA mr1670_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
vg1221512382 NA 8.90E-13 mr1853_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
vg1221512382 NA 9.76E-07 mr1853_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
vg1221512382 NA 4.51E-11 mr1942_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