| Variant ID: vg0317761625 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761625 |
| Reference Allele: G | Alternative Allele: GTAGATCACTCGT,GATCACTCGT |
| Primary Allele: G | Secondary Allele: GTAGATCACTCGT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 80. )
CTCTAAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAACT[G/GTAGATCACTCGT,GATCACTCGT]
TTGGAAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCAT
ATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTTCCAA[C/ACGAGTGATCTAC,ACGAGTGATC]
AGTTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTTAGAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTAGATCACTCGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.10% | 0.10% | 2.60% | 64.18% | GATCACTCGT: 0.04% |
| All Indica | 2759 | 5.00% | 0.10% | 3.23% | 91.52% | GATCACTCGT: 0.07% |
| All Japonica | 1512 | 85.20% | 0.00% | 0.26% | 14.55% | NA |
| Aus | 269 | 3.00% | 0.40% | 8.55% | 88.10% | NA |
| Indica I | 595 | 2.90% | 0.00% | 6.89% | 89.92% | GATCACTCGT: 0.34% |
| Indica II | 465 | 6.50% | 0.20% | 2.15% | 91.18% | NA |
| Indica III | 913 | 4.90% | 0.10% | 1.42% | 93.54% | NA |
| Indica Intermediate | 786 | 6.00% | 0.30% | 3.18% | 90.59% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.70% | 0.00% | 0.60% | 35.71% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.00% | 0.41% | 15.77% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 4.17% | 11.46% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 3.33% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761625 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761625 | G -> GTAGATCACTCGT | LOC_Os03g31190.1 | stop_gained&inframe_insertion ; p.Pro147_Thr148insAsnGluTerSer; HIGH | inframe_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761625 | G -> GATCACTCGT | LOC_Os03g31190.1 | stop_gained&inframe_insertion ; p.Thr148delinsAsnGluTerSer; HIGH | inframe_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |