| Variant ID: vg0710349296 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10349296 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGAGCAGATGGAGGCTAGCTTGATTGAGAGGGGTATCGAACCGGCAACAGCCAATTGGCCGGAACAATCAAAGTTCTGGTACTATGCTCACGGTGGAAC[G/A]
CTCAACCCAGCTGATGGCTCACTGGTCTTCGGCTATCAGATACGAGAGGCTGCGCGACGACTAACAGATGCAGTGGAAGCCTCCTCTCAGGGCACGTTCC
GGAACGTGCCCTGAGAGGAGGCTTCCACTGCATCTGTTAGTCGTCGCGCAGCCTCTCGTATCTGATAGCCGAAGACCAGTGAGCCATCAGCTGGGTTGAG[C/T]
GTTCCACCGTGAGCATAGTACCAGAACTTTGATTGTTCCGGCCAATTGGCTGTTGCCGGTTCGATACCCCTCTCAATCAAGCTAGCCTCCATCTGCTCCC
| 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 | 31.40% | 0.10% | 3.96% | 64.52% | NA |
| All Indica | 2759 | 6.50% | 0.00% | 1.59% | 91.88% | NA |
| All Japonica | 1512 | 74.50% | 0.30% | 9.26% | 15.94% | NA |
| Aus | 269 | 51.30% | 0.00% | 0.74% | 47.96% | NA |
| Indica I | 595 | 7.90% | 0.00% | 1.34% | 90.76% | NA |
| Indica II | 465 | 6.20% | 0.00% | 0.65% | 93.12% | NA |
| Indica III | 913 | 1.00% | 0.00% | 1.97% | 97.04% | NA |
| Indica Intermediate | 786 | 12.10% | 0.00% | 1.91% | 86.01% | NA |
| Temperate Japonica | 767 | 62.50% | 0.00% | 13.56% | 23.99% | NA |
| Tropical Japonica | 504 | 88.70% | 1.00% | 1.39% | 8.93% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 12.03% | 4.98% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 1.04% | 95.83% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 0.00% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710349296 | G -> DEL | LOC_Os07g17510.1 | N | frameshift_variant | Average:4.695; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0710349296 | G -> A | LOC_Os07g17510.1 | synonymous_variant ; p.Thr289Thr; LOW | synonymous_codon | Average:4.695; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |