| Variant ID: vg0629027974 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 29027974 |
| Reference Allele: TACAGATA | Alternative Allele: T |
| Primary Allele: TACAGATA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCAATGGCCATTCGTGCGTGTTCGAATATAAACTAAATTGCCAGTTTTCTCTTATGAGCTAAAACATTTGAGTTAAACTGGTCGGTGCATGCAACTCGA[TACAGATA/T]
AGTGAGTGTGAGTTACCAGGAAGACGGAGTCTCTAGTGGCGAGGGCCAAGATGTCGGCGCAGGACACCCTGTTCCGGCATTGGGGGTCGCTGTCGACGGC
GCCGTCGACAGCGACCCCCAATGCCGGAACAGGGTGTCCTGCGCCGACATCTTGGCCCTCGCCACTAGAGACTCCGTCTTCCTGGTAACTCACACTCACT[TATCTGTA/A]
TCGAGTTGCATGCACCGACCAGTTTAACTCAAATGTTTTAGCTCATAAGAGAAAACTGGCAATTTAGTTTATATTCGAACACGCACGAATGGCCATTGAT
| Populations | Population Size | Frequency of TACAGATA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.70% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.20% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.70% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.40% | 0.43% | 0.00% | NA |
| Indica III | 913 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027974 | TACAGATA -> T | LOC_Os06g48000.1 | downstream_gene_variant ; 4483.0bp to feature; MODIFIER | N | Average:67.405; most accessible tissue: Minghui63 root, score: 77.832 | N | N | N | N |
| vg0629027974 | TACAGATA -> T | LOC_Os06g48010.1 | intron_variant ; MODIFIER | N | Average:67.405; most accessible tissue: Minghui63 root, score: 77.832 | N | N | N | N |