| Variant ID: vg0409515304 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515304 |
| Reference Allele: G | Alternative Allele: GA |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
ATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCC[G/GA]
AAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTC
GACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTT[C/TC]
GGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.40% | 0.00% | 0.15% | 8.42% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 74.60% | 0.00% | 0.46% | 24.93% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 34.50% | 0.00% | 1.19% | 64.29% | NA |
| Japonica Intermediate | 241 | 82.20% | 0.00% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515304 | G -> GA | LOC_Os04g17380.1 | frameshift_variant ; p.Ser101fs; HIGH | N | Average:26.405; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0409515304 | G -> GA | LOC_Os04g17370.1 | downstream_gene_variant ; 626.0bp to feature; MODIFIER | N | Average:26.405; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0409515304 | G -> GA | LOC_Os04g17390.1 | downstream_gene_variant ; 1174.0bp to feature; MODIFIER | N | Average:26.405; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |