| Variant ID: vg1224769193 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 24769193 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTTCTCGGCCTCTACAAAAGACCGAGGCTCACCGTCGTCGCACGCAAGGTGCAACTGCGCCTCTAGGTCGCGAGGCACCAGTCCCGGCACCGGCTGGTC[G/A]
CCGAGAAGATCCTCTATCGTACGGTACCGTAGCTGCTCGCCATCGTGGTACGCGTCGATGCGCTCCCCGTCGTGGGAGAGCGGAGTAGCGAACTCCACCG
CGGTGGAGTTCGCTACTCCGCTCTCCCACGACGGGGAGCGCATCGACGCGTACCACGATGGCGAGCAGCTACGGTACCGTACGATAGAGGATCTTCTCGG[C/T]
GACCAGCCGGTGCCGGGACTGGTGCCTCGCGACCTAGAGGCGCAGTTGCACCTTGCGTGCGACGACGGTGAGCCTCGGTCTTTTGTAGAGGCCGAGAAAC
| 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 | 21.00% | 13.20% | 6.07% | 59.69% | NA |
| All Indica | 2759 | 5.80% | 6.10% | 9.39% | 78.72% | NA |
| All Japonica | 1512 | 53.50% | 24.00% | 0.33% | 22.16% | NA |
| Aus | 269 | 1.10% | 0.00% | 6.69% | 92.19% | NA |
| Indica I | 595 | 3.90% | 0.70% | 6.72% | 88.74% | NA |
| Indica II | 465 | 5.80% | 0.20% | 10.97% | 83.01% | NA |
| Indica III | 913 | 6.40% | 12.30% | 11.83% | 69.55% | NA |
| Indica Intermediate | 786 | 6.70% | 6.40% | 7.63% | 79.26% | NA |
| Temperate Japonica | 767 | 91.50% | 4.70% | 0.00% | 3.78% | NA |
| Tropical Japonica | 504 | 4.20% | 39.30% | 0.79% | 55.75% | NA |
| Japonica Intermediate | 241 | 35.70% | 53.50% | 0.41% | 10.37% | NA |
| VI/Aromatic | 96 | 1.00% | 86.50% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 20.00% | 14.40% | 4.44% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1224769193 | G -> DEL | LOC_Os12g40060.1 | N | frameshift_variant | Average:21.107; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg1224769193 | G -> A | LOC_Os12g40060.1 | synonymous_variant ; p.Gly995Gly; LOW | synonymous_codon | Average:21.107; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1224769193 | 4.15E-07 | NA | mr1334 | 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 |
| vg1224769193 | NA | 4.57E-07 | mr1183_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 |
| vg1224769193 | 8.13E-06 | NA | mr1334_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 |
| vg1224769193 | NA | 1.14E-08 | mr1794_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 |
| vg1224769193 | NA | 4.02E-06 | mr1865_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 |