| Variant ID: vg0727003261 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 27003261 |
| Reference Allele: A | Alternative Allele: ACAACTGAACATAG,ACAACTGAACATAGAGTCG,ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG,AC |
| Primary Allele: A | Secondary Allele: AC |
Inferred Ancestral Allele: Not determined.
TGCTTGATGCTATAGAGGACCTCCAGAATAACCCTCAAGAACAAGAACCACACACATGGAGAGACATACAAAGCAGGTGGTGCATCGAACACCTTACTGA[A/ACAACTGAACATAG,ACAACTGAACATAGAGTCG,ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG,AC]
AACTTATCTGCACATTTTGGTGGCAAGAAGTCGGCGGTGCTGTTCAATAAACTCTGTCAGCAGAGCCAACCAAGTAAGTTTACTGATATCTGGAAGGACC
GGTCCTTCCAGATATCAGTAAACTTACTTGGTTGGCTCTGCTGACAGAGTTTATTGAACAGCACCGCCGACTTCTTGCCACCAAAATGTGCAGATAAGTT[T/CTATGTTCAGTTGT,CGACTCTATGTTCAGTTGT,CGGGGGCTACACAAATACAAGGCTCGACTCTATGTTCAGTTGT,GT]
TCAGTAAGGTGTTCGATGCACCACCTGCTTTGTATGTCTCTCCATGTGTGTGGTTCTTGTTCTTGAGGGTTATTCTGGAGGTCCTCTATAGCATCAAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 0.50% | 0.83% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.23%; ACAACTGAACATAGAGTCG: 0.21%; ACAACTGAACATAG: 0.15% |
| All Indica | 2759 | 99.60% | 0.10% | 0.14% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.11%; ACAACTGAACATAG: 0.04% |
| All Japonica | 1512 | 94.80% | 1.40% | 2.25% | 0.00% | ACAACTGAACATAGAGTCG: 0.66%; ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.46%; ACAACTGAACATAG: 0.40% |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.37% |
| Indica I | 595 | 99.50% | 0.20% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.22% |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.00% | ACAACTGAACATAG: 0.11% |
| Indica Intermediate | 786 | 99.20% | 0.30% | 0.25% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.25% |
| Temperate Japonica | 767 | 95.60% | 1.30% | 2.61% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.26%; ACAACTGAACATAGAGTCG: 0.26% |
| Tropical Japonica | 504 | 92.30% | 2.00% | 2.58% | 0.00% | ACAACTGAACATAGAGTCG: 1.39%; ACAACTGAACATAG: 1.19%; ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.60% |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.41% | 0.00% | ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG: 0.83%; ACAACTGAACATAGAGTCG: 0.41% |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727003261 | A -> ACAACTGAACATAGAGTCGAGCCTTGTATT TGTGTAGCCCCCG | LOC_Os07g45250.1 | stop_gained&inframe_insertion ; p.Glu399_Asn400insGlnLeuAsnIle GluSerSerLeuValPheValTerProPro; HIGH | inframe_variant | Average:60.987; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003261 | A -> AC | LOC_Os07g45250.1 | frameshift_variant ; p.Asn400fs; HIGH | frameshift_variant | Average:60.987; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003261 | A -> ACAACTGAACATAGAGTCG | LOC_Os07g45250.1 | inframe_insertion ; p.Glu399_Asn400insGlnLeuAsnIle GluSer; MODERATE | inframe_variant | Average:60.987; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003261 | A -> ACAACTGAACATAG | LOC_Os07g45250.1 | frameshift_variant ; p.Asn400fs; HIGH | frameshift_variant | Average:60.987; most accessible tissue: Callus, score: 87.142 | N | N | N | N |