| Variant ID: vg0620602852 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602852 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTGCGAGACAGATTCTGTCTTTCCTTCTTCCCAGTTACTCGTATTACTGCCCTTCGAGTAGAAATTCTCAGTTTCAATCGGTGCAGCCTGTCCAGATTCA[C/G]
TAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTGCTACTGCAACATTTCCATATAGGTTTGGATAAGGAGTCTGCATTCTATCTGGAC
GTCCAGATAGAATGCAGACTCCTTATCCAAACCTATATGGAAATGTTGCAGTAGCACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTA[G/C]
TGAATCTGGACAGGCTGCACCGATTGAAACTGAGAATTTCTACTCGAAGGGCAGTAATACGAGTAACTGGGAAGAAGGAAAGACAGAATCTGTCTCGCAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.70% | 0.10% | 45.96% | 53.24% | NA |
| All Indica | 2759 | 0.00% | 0.20% | 37.77% | 62.02% | NA |
| All Japonica | 1512 | 2.10% | 0.10% | 55.03% | 42.86% | NA |
| Aus | 269 | 0.00% | 0.00% | 65.06% | 34.94% | NA |
| Indica I | 595 | 0.00% | 0.00% | 11.43% | 88.57% | NA |
| Indica II | 465 | 0.00% | 0.60% | 47.53% | 51.83% | NA |
| Indica III | 913 | 0.00% | 0.00% | 50.82% | 49.18% | NA |
| Indica Intermediate | 786 | 0.00% | 0.40% | 36.77% | 62.85% | NA |
| Temperate Japonica | 767 | 4.00% | 0.00% | 35.46% | 60.50% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 86.90% | 13.10% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 50.62% | 48.96% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 82.29% | 17.71% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 48.89% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602852 | C -> G | LOC_Os06g35340.1 | missense_variant ; p.Thr99Ser; MODERATE | nonsynonymous_codon ; T99S | Average:15.595; most accessible tissue: Minghui63 flag leaf, score: 22.094 | unknown | unknown | TOLERATED | 0.19 |
| vg0620602852 | C -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:15.595; most accessible tissue: Minghui63 flag leaf, score: 22.094 | N | N | N | N |