| Variant ID: vg1209004584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004584 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGA[G/C]
GCAGCTGGCAGTGTAGAATATGTCATTATCAGCCATGGCGATAAAGACAACATGTTTGGATAAATCCAATACACGGTATGGTAGGCGGAGCCTGCAGCTT
AAGCTGCAGGCTCCGCCTACCATACCGTGTATTGGATTTATCCAAACATGTTGTCTTTATCGCCATGGCTGATAATGACATATTCTACACTGCCAGCTGC[C/G]
TCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.10% | 1.20% | 0.47% | 21.22% | NA |
| All Indica | 2759 | 64.20% | 1.00% | 0.80% | 34.07% | NA |
| All Japonica | 1512 | 98.90% | 0.10% | 0.00% | 1.06% | NA |
| Aus | 269 | 86.60% | 0.40% | 0.00% | 13.01% | NA |
| Indica I | 595 | 57.80% | 0.20% | 1.01% | 41.01% | NA |
| Indica II | 465 | 65.20% | 0.00% | 0.86% | 33.98% | NA |
| Indica III | 913 | 65.80% | 1.80% | 0.55% | 31.87% | NA |
| Indica Intermediate | 786 | 66.40% | 1.30% | 0.89% | 31.42% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 65.60% | 30.20% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004584 | G -> C | LOC_Os12g15770.1 | synonymous_variant ; p.Ala18Ala; LOW | synonymous_codon | Average:46.048; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| vg1209004584 | G -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:46.048; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |