| Variant ID: vg1216438393 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16438393 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTCCGTCTGACCATCTGTTTGAGGGTGATAAGCGGTACTGAAATTCAAACGGGTACCCATCTCTACTTGTAATTTCTGCCAAAACTTTGAAGTAAACTG[G/A]
CTACCTCTATCTGACACTATCTTCTTAGGAACACCATGCAAGCATACCACTCTGGCCATGTATAACTCTGCAAGCTTATTCCCCGTGTAAGTTGTTTTGA
TCAAAACAACTTACACGGGGAATAAGCTTGCAGAGTTATACATGGCCAGAGTGGTATGCTTGCATGGTGTTCCTAAGAAGATAGTGTCAGATAGAGGTAG[C/T]
CAGTTTACTTCAAAGTTTTGGCAGAAATTACAAGTAGAGATGGGTACCCGTTTGAATTTCAGTACCGCTTATCACCCTCAAACAGATGGTCAGACGGAAA
| 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 | 62.10% | 1.90% | 24.74% | 11.26% | NA |
| All Indica | 2759 | 58.80% | 2.80% | 30.37% | 8.12% | NA |
| All Japonica | 1512 | 62.90% | 0.70% | 17.46% | 18.92% | NA |
| Aus | 269 | 90.70% | 0.00% | 7.81% | 1.49% | NA |
| Indica I | 595 | 57.50% | 0.80% | 31.43% | 10.25% | NA |
| Indica II | 465 | 46.00% | 4.30% | 42.80% | 6.88% | NA |
| Indica III | 913 | 67.00% | 2.60% | 23.88% | 6.46% | NA |
| Indica Intermediate | 786 | 57.60% | 3.40% | 29.77% | 9.16% | NA |
| Temperate Japonica | 767 | 83.80% | 0.40% | 7.69% | 8.08% | NA |
| Tropical Japonica | 504 | 29.00% | 0.80% | 32.54% | 37.70% | NA |
| Japonica Intermediate | 241 | 67.20% | 1.70% | 17.01% | 14.11% | NA |
| VI/Aromatic | 96 | 62.50% | 3.10% | 30.21% | 4.17% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 18.89% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216438393 | G -> DEL | LOC_Os12g27880.1 | N | frameshift_variant | Average:18.583; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| vg1216438393 | G -> A | LOC_Os12g27880.1 | synonymous_variant ; p.Ser1190Ser; LOW | synonymous_codon | Average:18.583; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216438393 | NA | 9.69E-06 | mr1613 | 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 |
| vg1216438393 | 2.89E-06 | 3.35E-07 | mr1071_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 |
| vg1216438393 | 4.69E-06 | 8.92E-07 | mr1203_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 |
| vg1216438393 | NA | 5.20E-07 | mr1613_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 |