| Variant ID: vg1216455900 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16455900 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGAGGAGGGTGTCGAGGAGAGTGATTGCTGCAACCGCGTTCTGCTGGGGGGTGCGAAAGACCGCTGTCCCATCGACGTCTTGTTGCCCAATGAGCTCTCT[C/T]
GCTCGCTGCCCAGATTCCAAGATGTGCTGTCGTCGGTCTTCAGCCTCCTTTGCAATCTGTTCGCGATCCTGTTGCTCACGCTGTAGTCGTTCTCGCTCTT
AAGAGCGAGAACGACTACAGCGTGAGCAACAGGATCGCGAACAGATTGCAAAGGAGGCTGAAGACCGACGACAGCACATCTTGGAATCTGGGCAGCGAGC[G/A]
AGAGAGCTCATTGGGCAACAAGACGTCGATGGGACAGCGGTCTTTCGCACCCCCCAGCAGAACGCGGTTGCAGCAATCACTCTCCTCGACACCCTCCTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.80% | 7.20% | 30.85% | 21.16% | NA |
| All Indica | 2759 | 34.10% | 0.80% | 41.61% | 23.49% | NA |
| All Japonica | 1512 | 49.90% | 19.00% | 12.17% | 18.85% | NA |
| Aus | 269 | 70.30% | 6.30% | 21.56% | 1.86% | NA |
| Indica I | 595 | 30.30% | 0.20% | 35.29% | 34.29% | NA |
| Indica II | 465 | 38.30% | 2.20% | 35.91% | 23.66% | NA |
| Indica III | 913 | 33.20% | 0.20% | 47.86% | 18.73% | NA |
| Indica Intermediate | 786 | 35.80% | 1.00% | 42.49% | 20.74% | NA |
| Temperate Japonica | 767 | 79.80% | 11.00% | 1.56% | 7.69% | NA |
| Tropical Japonica | 504 | 6.50% | 27.00% | 31.55% | 34.92% | NA |
| Japonica Intermediate | 241 | 45.60% | 28.20% | 5.39% | 20.75% | NA |
| VI/Aromatic | 96 | 8.30% | 4.20% | 35.42% | 52.08% | NA |
| Intermediate | 90 | 40.00% | 8.90% | 37.78% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216455900 | C -> DEL | LOC_Os12g27910.1 | N | frameshift_variant | Average:17.733; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |
| vg1216455900 | C -> T | LOC_Os12g27910.1 | synonymous_variant ; p.Ala266Ala; LOW | synonymous_codon | Average:17.733; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216455900 | 6.77E-06 | 6.25E-06 | mr1219 | 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 |
| vg1216455900 | 4.39E-07 | 1.64E-07 | mr1201_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 |
| vg1216455900 | 1.66E-07 | 1.84E-07 | mr1219_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 |