| Variant ID: vg0112387565 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12387565 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTTGATCTGCCGGTATGACCGTGCCGGTGCTGTCGGTCTGGCCGGTGTAGATCGCCTAGTCTAATCGTCCCGAAGTCACCTCTGCCTCTTGACGACGTC[G/A]
CCGGTCTGACCGCCAGTGTCCAGCCGGTCTGACCGCCGCAATGCCGCAGGTCTGACCACCGGTAACTCTCCAGTTAGACCGCCGAACCCGAGCAAATACA
TGTATTTGCTCGGGTTCGGCGGTCTAACTGGAGAGTTACCGGTGGTCAGACCTGCGGCATTGCGGCGGTCAGACCGGCTGGACACTGGCGGTCAGACCGG[C/T]
GACGTCGTCAAGAGGCAGAGGTGACTTCGGGACGATTAGACTAGGCGATCTACACCGGCCAGACCGACAGCACCGGCACGGTCATACCGGCAGATCAACC
| 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 | 90.90% | 3.50% | 0.44% | 5.12% | NA |
| All Indica | 2759 | 96.30% | 0.00% | 0.62% | 3.08% | NA |
| All Japonica | 1512 | 89.20% | 10.70% | 0.00% | 0.07% | NA |
| Aus | 269 | 42.40% | 0.00% | 1.49% | 56.13% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 0.00% | 0.86% | 2.58% | NA |
| Indica III | 913 | 95.80% | 0.00% | 0.99% | 3.18% | NA |
| Indica Intermediate | 786 | 93.80% | 0.10% | 0.51% | 5.60% | NA |
| Temperate Japonica | 767 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.50% | 6.30% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 63.90% | 36.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112387565 | G -> A | LOC_Os01g22050.1 | N | stop_gained | Average:62.336; most accessible tissue: Callus, score: 86.386 | N | N | N | N |
| vg0112387565 | G -> DEL | LOC_Os01g22050.1 | N | frameshift_variant | Average:62.336; most accessible tissue: Callus, score: 86.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0112387565 | NA | 4.59E-07 | mr1064 | 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 |
| vg0112387565 | 3.53E-06 | 3.53E-06 | mr1066 | 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 |
| vg0112387565 | NA | 8.46E-06 | mr1534 | 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 |