| Variant ID: vg0317761982 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761982 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAGGAGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCA[C/G]
CAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCG
CGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTG[G/C]
TGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCTCCTG
| 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 | 50.80% | 0.20% | 6.35% | 42.64% | NA |
| All Indica | 2759 | 34.50% | 0.40% | 8.34% | 56.76% | NA |
| All Japonica | 1512 | 85.40% | 0.00% | 1.12% | 13.49% | NA |
| Aus | 269 | 5.90% | 0.00% | 15.99% | 78.07% | NA |
| Indica I | 595 | 9.20% | 0.30% | 9.92% | 80.50% | NA |
| Indica II | 465 | 29.50% | 0.00% | 5.59% | 64.95% | NA |
| Indica III | 913 | 54.90% | 0.80% | 8.65% | 35.71% | NA |
| Indica Intermediate | 786 | 33.00% | 0.30% | 8.40% | 58.40% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 63.70% | 0.00% | 3.17% | 33.13% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.00% | 0.41% | 14.94% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 6.25% | 7.29% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 4.44% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761982 | C -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317761982 | C -> G | LOC_Os03g31190.1 | missense_variant ; p.Gly29Ala; MODERATE | nonsynonymous_codon ; G29A | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | unknown | unknown | DELETERIOUS | 0.01 |