| Variant ID: vg0811599014 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599014 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCGCCGGCCTCGTCGTTGCTGTCGTCCGCACCATCGTCACCGCCCTCCTCGTCGGAGTCGAGGGCGAACGCGAGCTGAGGGGCCGTACCCTCGAAGCTGT[G/T]
GACGATGTGGTCGGCGGCGTCCCGGACCTGCGCGCGCGCGCCGTCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTCAGGGTCC
GGACCCTGACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGACGGCGCGCGCGCGCAGGTCCGGGACGCCGCCGACCACATCGTC[C/A]
ACAGCTTCGAGGGTACGGCCCCTCAGCTCGCGTTCGCCCTCGACTCCGACGAGGAGGGCGGTGACGATGGTGCGGACGACAGCAACGACGAGGCCGGCGA
| 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 | 37.50% | 0.40% | 2.48% | 59.65% | NA |
| All Indica | 2759 | 24.20% | 0.70% | 2.25% | 72.82% | NA |
| All Japonica | 1512 | 60.80% | 0.00% | 3.44% | 35.71% | NA |
| Aus | 269 | 42.40% | 0.00% | 0.00% | 57.62% | NA |
| Indica I | 595 | 12.40% | 0.20% | 0.67% | 86.72% | NA |
| Indica II | 465 | 12.50% | 0.00% | 0.65% | 86.88% | NA |
| Indica III | 913 | 41.00% | 1.60% | 4.16% | 53.23% | NA |
| Indica Intermediate | 786 | 20.60% | 0.50% | 2.16% | 76.72% | NA |
| Temperate Japonica | 767 | 84.90% | 0.00% | 0.65% | 14.47% | NA |
| Tropical Japonica | 504 | 33.70% | 0.00% | 5.75% | 60.52% | NA |
| Japonica Intermediate | 241 | 41.10% | 0.00% | 7.47% | 51.45% | NA |
| VI/Aromatic | 96 | 35.40% | 0.00% | 1.04% | 63.54% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 2.22% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599014 | G -> T | LOC_Os08g19400.1 | missense_variant ; p.His297Asn; MODERATE | nonsynonymous_codon ; H297N | Average:19.08; most accessible tissue: Zhenshan97 flower, score: 30.815 | unknown | unknown | TOLERATED | 0.12 |
| vg0811599014 | G -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:19.08; most accessible tissue: Zhenshan97 flower, score: 30.815 | N | N | N | N |