| Variant ID: vg1215688513 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15688513 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCAGTTATCCGCCCCCAACGCCAGTTCTACAACAACAATACTGGTAATCGTGGCAATGACAACCGCAACATGGTTGCTCGTCCTGTAGCAACTCTAGCTC[A/C]
GAACCAGCCCGTCAGGAAGGAACAGGGAAGCAAGCCAGGGGTATGCTTCAATTGTGGGGATCCAGGACATTATGCTGATAAGTGTCCTAAGCCTCGACGC
GCGTCGAGGCTTAGGACACTTATCAGCATAATGTCCTGGATCCCCACAATTGAAGCATACCCCTGGCTTGCTTCCCTGTTCCTTCCTGACGGGCTGGTTC[T/G]
GAGCTAGAGTTGCTACAGGACGAGCAACCATGTTGCGGTTGTCATTGCCACGATTACCAGTATTGTTGTTGTAGAACTGGCGTTGGGGGCGGATAACTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.70% | 5.70% | 4.74% | 2.86% | NA |
| All Indica | 2759 | 92.20% | 1.80% | 2.65% | 3.26% | NA |
| All Japonica | 1512 | 73.90% | 13.80% | 9.52% | 2.71% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 89.10% | 1.00% | 2.35% | 7.56% | NA |
| Indica II | 465 | 90.50% | 1.90% | 4.95% | 2.58% | NA |
| Indica III | 913 | 95.80% | 1.50% | 1.42% | 1.20% | NA |
| Indica Intermediate | 786 | 91.50% | 2.80% | 2.93% | 2.80% | NA |
| Temperate Japonica | 767 | 95.40% | 0.10% | 3.00% | 1.43% | NA |
| Tropical Japonica | 504 | 39.90% | 35.50% | 20.63% | 3.97% | NA |
| Japonica Intermediate | 241 | 76.80% | 12.00% | 7.05% | 4.15% | NA |
| VI/Aromatic | 96 | 92.70% | 3.10% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215688513 | A -> C | LOC_Os12g26780.1 | missense_variant ; p.Gln303Pro; MODERATE | nonsynonymous_codon ; Q303P | Average:27.459; most accessible tissue: Zhenshan97 root, score: 50.453 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1215688513 | A -> DEL | LOC_Os12g26780.1 | N | frameshift_variant | Average:27.459; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215688513 | 1.41E-07 | 1.08E-10 | mr1583 | 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 |
| vg1215688513 | 7.45E-06 | NA | mr1754 | 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 |
| vg1215688513 | NA | 9.75E-08 | mr1124_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 |
| vg1215688513 | 8.25E-06 | 1.89E-06 | 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 |
| vg1215688513 | NA | 5.89E-06 | mr1583_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 |
| vg1215688513 | 2.11E-08 | 7.42E-10 | mr1850_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 |