| Variant ID: vg0301458683 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 1458683 |
| Reference Allele: GTTGGAC | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: GTTGGAC |
Inferred Ancestral Allele: Not determined.
CTTGTTCATCGGTTTCTTTGGCTGTTTGCTCCGGTTGTATTCTTGTTCATCGAATTGATACGCAGATCTCTAATCTTATCTTCTTCTGCGATAATGGGTT[GTTGGAC/G]
TTGGATATGATCAGTCTGATGGACCAGGAAGTGAGCTGTCAAAAACTGTGAATTTCCATTTGAAGAAGGGAAAGATCCTTTTTTTTTTCTAGTGTATTTG
CAAATACACTAGAAAAAAAAAAGGATCTTTCCCTTCTTCAAATGGAAATTCACAGTTTTTGACAGCTCACTTCCTGGTCCATCAGACTGATCATATCCAA[GTCCAAC/C]
AACCCATTATCGCAGAAGAAGATAAGATTAGAGATCTGCGTATCAATTCGATGAACAAGAATACAACCGGAGCAAACAGCCAAAGAAACCGATGAACAAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTTGGAC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.60% | 13.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 61.20% | 38.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 46.20% | 53.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 82.50% | 17.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 64.30% | 35.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 13.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0301458683 | GTTGGAC -> G | LOC_Os03g03420.1 | downstream_gene_variant ; 4815.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301458683 | GTTGGAC -> G | LOC_Os03g03420.2 | downstream_gene_variant ; 4815.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301458683 | GTTGGAC -> G | LOC_Os03g03410.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |