Search for Variation information by Variation ID:
Detailed information for vg1215688504:
| Variant ID: vg1215688504 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15688504 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGATCTTCATCAGTTATCCGCCCCCAACGCCAGTTCTACAACAACAATACTGGTAATCGTGGCAATGACAACCGCAACATGGTTGCTCGTCCTGTAGCAA[C/A]
TCTAGCTCAGAACCAGCCCGTCAGGAAGGAACAGGGAAGCAAGCCAGGGGTATGCTTCAATTGTGGGGATCCAGGACATTATGCTGATAAGTGTCCTAAG
Reverse complement sequence
CTTAGGACACTTATCAGCATAATGTCCTGGATCCCCACAATTGAAGCATACCCCTGGCTTGCTTCCCTGTTCCTTCCTGACGGGCTGGTTCTGAGCTAGA[G/T]
TTGCTACAGGACGAGCAACCATGTTGCGGTTGTCATTGCCACGATTACCAGTATTGTTGTTGTAGAACTGGCGTTGGGGGCGGATAACTGATGAAGATCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.50% | 7.20% | 3.68% | 3.70% | NA |
| All Indica | 2759 | 90.70% | 2.00% | 2.43% | 4.86% | NA |
| All Japonica | 1512 | 73.10% | 17.90% | 6.61% | 2.38% | NA |
| Aus | 269 | 98.90% | 0.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 88.70% | 1.20% | 1.68% | 8.40% | NA |
| Indica II | 465 | 87.50% | 1.90% | 4.09% | 6.45% | NA |
| Indica III | 913 | 94.30% | 1.80% | 1.86% | 2.08% | NA |
| Indica Intermediate | 786 | 89.90% | 2.90% | 2.67% | 4.45% | NA |
| Temperate Japonica | 767 | 95.60% | 0.80% | 2.35% | 1.30% | NA |
| Tropical Japonica | 504 | 37.50% | 45.40% | 13.49% | 3.57% | NA |
| Japonica Intermediate | 241 | 76.30% | 14.50% | 5.81% | 3.32% | NA |
| VI/Aromatic | 96 | 90.60% | 3.10% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 85.60% | 10.00% | 1.11% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215688504 | C -> DEL | LOC_Os12g26780.1 | N | frameshift_variant | Average:27.57; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg1215688504 | C -> A | LOC_Os12g26780.1 | missense_variant ; p.Thr300Asn; MODERATE | nonsynonymous_codon ; T300N | Average:27.57; most accessible tissue: Zhenshan97 root, score: 50.453 | possibly damaging  |
1.938 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215688504 | 6.26E-06 | 1.70E-08 | mr1583 | 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 |
| vg1215688504 | 8.09E-07 | 8.09E-07 | mr1929 | 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 |
| vg1215688504 | NA | 4.13E-06 | mr1124_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 |
| vg1215688504 | 2.56E-06 | 2.33E-07 | mr1498_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 |
| vg1215688504 | NA | 2.21E-06 | mr1850_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 |