| Variant ID: vg1209903866 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9903866 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCCATAGAAATTCAGTATCCCACGGAAGAACGTTGAGGTTGGAAGAGCAAATCCACCATAAAAGAAATGAGAGAAGACCACGACCTCATGTGTATCGGG[G/A]
GTCGGAAAAGCCTCACCGCACGCTGGCCGCCACCCGATGATCTCCTTGGCAGGGAGAACGCCGTGCGCCACCATCTCCTTCAGGTTCTCCTCCGTCACGT
ACGTGACGGAGGAGAACCTGAAGGAGATGGTGGCGCACGGCGTTCTCCCTGCCAAGGAGATCATCGGGTGGCGGCCAGCGTGCGGTGAGGCTTTTCCGAC[C/T]
CCCGATACACATGAGGTCGTGGTCTTCTCTCATTTCTTTTATGGTGGATTTGCTCTTCCAACCTCAACGTTCTTCCGTGGGATACTGAATTTCTATGGAA
| 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 | 33.00% | 3.50% | 30.15% | 33.39% | NA |
| All Indica | 2759 | 13.50% | 0.30% | 38.31% | 47.95% | NA |
| All Japonica | 1512 | 71.60% | 10.10% | 12.50% | 5.82% | NA |
| Aus | 269 | 14.90% | 0.00% | 46.10% | 39.03% | NA |
| Indica I | 595 | 14.80% | 0.20% | 28.24% | 56.81% | NA |
| Indica II | 465 | 14.20% | 0.60% | 31.40% | 53.76% | NA |
| Indica III | 913 | 12.00% | 0.10% | 50.71% | 37.13% | NA |
| Indica Intermediate | 786 | 13.70% | 0.30% | 35.62% | 50.38% | NA |
| Temperate Japonica | 767 | 86.20% | 0.50% | 5.08% | 8.21% | NA |
| Tropical Japonica | 504 | 50.60% | 28.00% | 18.06% | 3.37% | NA |
| Japonica Intermediate | 241 | 69.30% | 2.90% | 24.48% | 3.32% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 41.67% | 42.71% | NA |
| Intermediate | 90 | 54.40% | 5.60% | 16.67% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209903866 | G -> DEL | LOC_Os12g17300.1 | N | frameshift_variant | Average:26.389; most accessible tissue: Minghui63 flag leaf, score: 62.47 | N | N | N | N |
| vg1209903866 | G -> A | LOC_Os12g17300.1 | synonymous_variant ; p.Thr49Thr; LOW | synonymous_codon | Average:26.389; most accessible tissue: Minghui63 flag leaf, score: 62.47 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209903866 | NA | 2.75E-08 | mr1696 | 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 |
| vg1209903866 | 1.76E-06 | 1.76E-06 | mr1848 | 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 |
| vg1209903866 | NA | 3.75E-06 | mr1218_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 |
| vg1209903866 | NA | 2.30E-06 | mr1422_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 |
| vg1209903866 | NA | 1.58E-06 | mr1653_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 |
| vg1209903866 | NA | 1.71E-08 | 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 |