| Variant ID: vg0322193997 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193997 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TACCCTCGAAGCTGTGGACGATGTAGTCGGCGGCGTCCCGGACCCGCGCGCGCGCGCCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGG[G/A]
GAGAAGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCT
AGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACTTCTC[C/T]
CCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGGCGCGCGCGCGCGGGTCCGGGACGCCGCCGACTACATCGTCCACAGCTTCGAGGGTA
| 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 | 38.80% | 0.10% | 2.29% | 58.80% | NA |
| All Indica | 2759 | 43.10% | 0.20% | 1.70% | 55.02% | NA |
| All Japonica | 1512 | 32.60% | 0.00% | 0.93% | 66.47% | NA |
| Aus | 269 | 39.00% | 0.40% | 12.64% | 47.96% | NA |
| Indica I | 595 | 22.00% | 0.00% | 0.84% | 77.14% | NA |
| Indica II | 465 | 29.50% | 0.00% | 2.15% | 68.39% | NA |
| Indica III | 913 | 69.70% | 0.30% | 1.53% | 28.48% | NA |
| Indica Intermediate | 786 | 36.30% | 0.30% | 2.29% | 61.20% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 58.50% | 0.00% | 0.99% | 40.48% | NA |
| Japonica Intermediate | 241 | 32.80% | 0.00% | 1.24% | 65.98% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 12.50% | 71.88% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 1.11% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193997 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Ser375Ser; LOW | synonymous_codon | Average:8.179; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0322193997 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:8.179; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |