Search for Variation information by Variation ID:
Detailed information for vg1213797975:
| Variant ID: vg1213797975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13797975 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
GGAAGAGCCTACTTTTAATCAAGTCATAAAGTTATCTCGAAAGGAAAATGCGGGATGCTTATCGAGTACACTTACATTGATAGCTTCATCACGTTCGGCC[G/A]
CCCCCTTTTCACAAAGGGGCACGGGGATGTCACTCGCCGTAGTCGGACCACTGATCATCACCTGGCCGACGCGGCGCTCCATGGCTTCGCTGTTCAGACC
Reverse complement sequence
GGTCTGAACAGCGAAGCCATGGAGCGCCGCGTCGGCCAGGTGATGATCAGTGGTCCGACTACGGCGAGTGACATCCCCGTGCCCCTTTGTGAAAAGGGGG[C/T]
GGCCGAACGTGATGAAGCTATCAATGTAAGTGTACTCGATAAGCATCCCGCATTTTCCTTTCGAGATAACTTTATGACTTGATTAAAAGTAGGCTCTTCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.30% | 5.60% | 0.97% | 8.08% | NA |
| All Indica | 2759 | 87.10% | 7.00% | 1.16% | 4.82% | NA |
| All Japonica | 1512 | 91.20% | 0.10% | 0.13% | 8.60% | NA |
| Aus | 269 | 29.00% | 24.50% | 3.35% | 43.12% | NA |
| Indica I | 595 | 88.20% | 3.40% | 0.84% | 7.56% | NA |
| Indica II | 465 | 90.80% | 2.60% | 1.72% | 4.95% | NA |
| Indica III | 913 | 85.30% | 11.80% | 0.33% | 2.52% | NA |
| Indica Intermediate | 786 | 86.00% | 6.60% | 2.04% | 5.34% | NA |
| Temperate Japonica | 767 | 88.10% | 0.00% | 0.26% | 11.60% | NA |
| Tropical Japonica | 504 | 97.00% | 0.20% | 0.00% | 2.78% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.00% | 11.20% | NA |
| VI/Aromatic | 96 | 93.80% | 3.10% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 2.22% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213797975 | G -> DEL | LOC_Os12g24210.1 | N | frameshift_variant | Average:52.862; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1213797975 | G -> A | LOC_Os12g24210.1 | missense_variant ; p.Ala245Val; MODERATE | nonsynonymous_codon ; A245V | Average:52.862; most accessible tissue: Minghui63 young leaf, score: 65.161 | benign  |
0.572 |
TOLERATED | 0.10 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213797975 | 2.18E-06 | 9.72E-06 | mr1057 | Ind_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 |
| vg1213797975 | NA | 9.45E-06 | mr1738 | 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 |
| vg1213797975 | 4.47E-06 | 2.04E-06 | mr1755 | 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 |