Variant ID: vg0135986444 (JBrowse) | Variation Type: INDEL |
Chromosome: chr01 | Position: 35986444 |
Reference Allele: TA | Alternative Allele: T,TAA |
Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGAACACATCATTCAACCGACCTACCTTTGAGCCACACTAATCATTTTCTGGATTTGCCAGTCAATCTATTGGAACCCAATCCCCTCACGTGTTTCCTT[TA/T,TAA]
AAAAAAAATATTAACAGCCAATCGGATGATGAAATTGGGGAAACTACCTGTGAACAGATGAGCTAATTACTTAAAAAAAACGCATATGCTACACTTTACA
TGTAAAGTGTAGCATATGCGTTTTTTTTAAGTAATTAGCTCATCTGTTCACAGGTAGTTTCCCCAATTTCATCATCCGATTGGCTGTTAATATTTTTTTT[TA/A,TTA]
AAGGAAACACGTGAGGGGATTGGGTTCCAATAGATTGACTGGCAAATCCAGAAAATGATTAGTGTGGCTCAAAGGTAGGTCGGTTGAATGATGTGTTCCG
Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 52.80% | 47.00% | 0.13% | 0.00% | TAA: 0.06% |
All Indica | 2759 | 27.30% | 72.60% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
Aus | 269 | 40.10% | 58.00% | 0.74% | 0.00% | TAA: 1.12% |
Indica I | 595 | 12.10% | 87.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 7.50% | 92.50% | 0.00% | 0.00% | NA |
Indica III | 913 | 40.90% | 59.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 34.70% | 64.80% | 0.51% | 0.00% | NA |
Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 65.60% | 34.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0135986444 | TA -> T | LOC_Os01g62160.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.112; most accessible tissue: Callus, score: 74.913 | N | N | N | N |
vg0135986444 | TA -> TAA | LOC_Os01g62160.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.112; most accessible tissue: Callus, score: 74.913 | N | N | N | N |