| Variant ID: vg0322194009 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194009 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTGGACGATGTAGTCGGCGGCGTCCCGGACCCGCGCGCGCGCGCCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTCAGG[G/A]
TCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCT
AGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGA[C/T]
CCTGACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGGCGCGCGCGCGCGGGTCCGGGACGCCGCCGACTACATCGTCCACA
| 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 | 40.00% | 0.10% | 1.10% | 58.84% | NA |
| All Indica | 2759 | 43.90% | 0.10% | 1.34% | 54.66% | NA |
| All Japonica | 1512 | 32.70% | 0.00% | 0.86% | 66.40% | NA |
| Aus | 269 | 46.80% | 0.00% | 0.37% | 52.79% | NA |
| Indica I | 595 | 22.00% | 0.00% | 0.84% | 77.14% | NA |
| Indica II | 465 | 28.80% | 0.90% | 2.37% | 67.96% | NA |
| Indica III | 913 | 71.00% | 0.00% | 1.10% | 27.93% | NA |
| Indica Intermediate | 786 | 37.80% | 0.00% | 1.40% | 60.81% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.91% | 83.57% | NA |
| Tropical Japonica | 504 | 58.50% | 0.00% | 0.99% | 40.48% | NA |
| Japonica Intermediate | 241 | 33.60% | 0.00% | 0.41% | 65.98% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 1.04% | 71.88% | NA |
| Intermediate | 90 | 35.60% | 0.00% | 0.00% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194009 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Asp371Asp; LOW | synonymous_codon | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0322194009 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |