| Variant ID: vg0100791472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791472 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCTGATGGTGGGCACAACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATC[G/A]
AAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGC
GCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTT[C/T]
GATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGTTGTGCCCACCATCAGCA
| 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 | 56.20% | 1.30% | 2.07% | 40.48% | NA |
| All Indica | 2759 | 50.00% | 1.50% | 2.46% | 46.03% | NA |
| All Japonica | 1512 | 72.80% | 0.30% | 1.19% | 25.66% | NA |
| Aus | 269 | 37.20% | 5.20% | 1.49% | 56.13% | NA |
| Indica I | 595 | 69.10% | 0.70% | 0.50% | 29.75% | NA |
| Indica II | 465 | 75.90% | 0.00% | 1.08% | 23.01% | NA |
| Indica III | 913 | 18.30% | 3.40% | 2.52% | 75.79% | NA |
| Indica Intermediate | 786 | 57.00% | 0.90% | 4.71% | 37.40% | NA |
| Temperate Japonica | 767 | 69.90% | 0.50% | 1.56% | 28.03% | NA |
| Tropical Japonica | 504 | 83.10% | 0.00% | 0.40% | 16.47% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.40% | 1.66% | 37.34% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 5.21% | 84.38% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 3.33% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791472 | G -> A | LOC_Os01g02440.1 | synonymous_variant ; p.Ser249Ser; LOW | synonymous_codon | Average:53.57; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0100791472 | G -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:53.57; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |