| Variant ID: vg0320570050 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 20570050 |
| Reference Allele: A | Alternative Allele: AGTCGTCGTC,AGTCGTC,AGTCGTCGTCGTC |
| Primary Allele: AGTCGTCGTC | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGACACCGCCATCGCATCAATCACCTCCGGAAGAAGGAACCTCGCCGCCACCTTCGCCATCATCAGGGGCTACAACACCTTCACCTCCCCCAAATGCGC[A/AGTCGTCGTC,AGTCGTC,AGTCGTCGTCGTC]
GTCGTCGTCGTCGTCTTCCACACCTCCTGCCGGCGCAGGAACCTCGCCACCTGCACCGCGCGAAATGCCATCGCCCGGGACGCCACCATCGCCGCCGACG
CGTCGGCGGCGATGGTGGCGTCCCGGGCGATGGCATTTCGCGCGGTGCAGGTGGCGAGGTTCCTGCGCCGGCAGGAGGTGTGGAAGACGACGACGACGAC[T/GACGACGACT,GACGACT,GACGACGACGACT]
GCGCATTTGGGGGAGGTGAAGGTGTTGTAGCCCCTGATGATGGCGAAGGTGGCGGCGAGGTTCCTTCTTCCGGAGGTGATTGATGCGATGGCGGTGTCGA
| Populations | Population Size | Frequency of AGTCGTCGTC(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 32.70% | 0.15% | 0.47% | AGTCGTCGTCGTC: 0.25%; AGTCGTC: 0.21% |
| All Indica | 2759 | 96.20% | 3.20% | 0.22% | 0.36% | AGTCGTC: 0.07% |
| All Japonica | 1512 | 11.80% | 86.80% | 0.00% | 0.46% | AGTCGTCGTCGTC: 0.79%; AGTCGTC: 0.07% |
| Aus | 269 | 85.90% | 13.40% | 0.37% | 0.00% | AGTCGTC: 0.37% |
| Indica I | 595 | 96.60% | 2.00% | 1.01% | 0.34% | NA |
| Indica II | 465 | 96.10% | 3.70% | 0.00% | 0.22% | NA |
| Indica III | 913 | 97.90% | 1.90% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 93.90% | 5.20% | 0.00% | 0.64% | AGTCGTC: 0.25% |
| Temperate Japonica | 767 | 0.30% | 99.60% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 31.50% | 65.50% | 0.00% | 0.60% | AGTCGTCGTCGTC: 2.38% |
| Japonica Intermediate | 241 | 7.50% | 90.90% | 0.00% | 1.24% | AGTCGTC: 0.41% |
| VI/Aromatic | 96 | 24.00% | 72.90% | 0.00% | 0.00% | AGTCGTC: 3.12% |
| Intermediate | 90 | 48.90% | 42.20% | 0.00% | 5.56% | AGTCGTC: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320570050 | A -> AGTCGTC | LOC_Os03g37120.1 | disruptive_inframe_insertion ; p.Ser157_Ser158dup; MODERATE | inframe_variant | Average:77.894; most accessible tissue: Zhenshan97 panicle, score: 87.126 | N | N | N | N |
| vg0320570050 | A -> AGTCGTCGTCGTC | LOC_Os03g37120.1 | disruptive_inframe_insertion ; p.Ser155_Ser158dup; MODERATE | inframe_variant | Average:77.894; most accessible tissue: Zhenshan97 panicle, score: 87.126 | N | N | N | N |
| vg0320570050 | A -> DEL | LOC_Os03g37120.1 | N | frameshift_variant | Average:77.894; most accessible tissue: Zhenshan97 panicle, score: 87.126 | N | N | N | N |
| vg0320570050 | A -> AGTCGTCGTC | LOC_Os03g37120.1 | disruptive_inframe_insertion ; p.Ser156_Ser158dup; MODERATE | inframe_variant | Average:77.894; most accessible tissue: Zhenshan97 panicle, score: 87.126 | N | N | N | N |