| Variant ID: vg0322194015 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194015 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGATGTAGTCGGCGGCGTCCCGGACCCGCGCGCGCGCGCCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTCAGGGTCCCT[G/A,T]
GCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTGGAGGG
CCCTCCAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGC[C/T,A]
AGGGACCCTGACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGGCGCGCGCGCGCGGGTCCGGGACGCCGCCGACTACATCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.80% | 0.20% | 0.89% | 59.04% | A: 0.02% |
| All Indica | 2759 | 43.80% | 0.30% | 0.94% | 54.95% | NA |
| All Japonica | 1512 | 32.70% | 0.00% | 0.86% | 66.40% | NA |
| Aus | 269 | 45.00% | 0.70% | 0.74% | 53.16% | A: 0.37% |
| Indica I | 595 | 21.80% | 0.20% | 0.84% | 77.14% | NA |
| Indica II | 465 | 30.50% | 0.20% | 0.86% | 68.39% | NA |
| Indica III | 913 | 70.40% | 0.40% | 0.77% | 28.37% | NA |
| Indica Intermediate | 786 | 37.40% | 0.30% | 1.27% | 61.07% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194015 | G -> T | LOC_Os03g39930.1 | synonymous_variant ; p.Ala369Ala; LOW | synonymous_codon | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0322194015 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Ala369Ala; LOW | synonymous_codon | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0322194015 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |