| Variant ID: vg1212666330 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666330 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTC[G/C]
CAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATC
GATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTG[C/G]
GACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCC
| 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 | 78.50% | 1.90% | 2.33% | 17.25% | NA |
| All Indica | 2759 | 80.30% | 1.90% | 2.43% | 15.37% | NA |
| All Japonica | 1512 | 71.90% | 2.40% | 2.45% | 23.28% | NA |
| Aus | 269 | 95.20% | 0.00% | 0.74% | 4.09% | NA |
| Indica I | 595 | 70.10% | 0.70% | 2.02% | 27.23% | NA |
| Indica II | 465 | 80.20% | 1.70% | 2.37% | 15.70% | NA |
| Indica III | 913 | 86.90% | 2.80% | 2.52% | 7.78% | NA |
| Indica Intermediate | 786 | 80.50% | 1.80% | 2.67% | 15.01% | NA |
| Temperate Japonica | 767 | 84.20% | 0.30% | 0.39% | 15.12% | NA |
| Tropical Japonica | 504 | 59.30% | 6.20% | 5.95% | 28.57% | NA |
| Japonica Intermediate | 241 | 58.90% | 1.20% | 1.66% | 38.17% | NA |
| VI/Aromatic | 96 | 86.50% | 1.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 75.60% | 2.20% | 2.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666330 | G -> C | LOC_Os12g22430.1 | synonymous_variant ; p.Ser265Ser; LOW | synonymous_codon | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666330 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |