| Variant ID: vg0317761624 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761624 |
| Reference Allele: TGTTGGAAA | Alternative Allele: TTGTAGATCACTCGTTGGAAA,T,TTATAGATCACTCGTTGGAAA,TTATAGTTGGAAA |
| Primary Allele: TGTTGGAAA | Secondary Allele: TTGTAGATCACTCGTTGGAA A |
Inferred Ancestral Allele: Not determined.
TCTCTAAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAAC[TGTTGGAAA/TTGTAGATCACTCGTTGGAAA,T,TTATAGATCACTCGTTGGAAA,TTATAGTTGGAAA]
TATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCATACTATGC
GCATAGTATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATA[TTTCCAACA/TTTCCAACGAGTGATCTACAA,A,TTTCCAACGAGTGATCTATAA,TTTCCAACTATAA]
GTTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTTAGAGA
| Populations | Population Size | Frequency of TGTTGGAAA(primary allele) | Frequency of TTGTAGATCACTCGTTGGAA A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.70% | 2.20% | 21.46% | 39.38% | TTATAGATCACTCGTTGGAAA: 0.13%; T: 0.13%; TTATAGTTGGAAA: 0.04% |
| All Indica | 2759 | 10.20% | 3.40% | 33.60% | 52.30% | TTATAGATCACTCGTTGGAAA: 0.22%; T: 0.22%; TTATAGTTGGAAA: 0.07% |
| All Japonica | 1512 | 86.20% | 0.00% | 1.46% | 12.30% | NA |
| Aus | 269 | 7.10% | 2.60% | 17.47% | 72.86% | NA |
| Indica I | 595 | 6.70% | 0.80% | 26.55% | 63.87% | TTATAGATCACTCGTTGGAAA: 1.01%; T: 0.67%; TTATAGTTGGAAA: 0.34% |
| Indica II | 465 | 11.60% | 3.20% | 33.98% | 50.97% | T: 0.22% |
| Indica III | 913 | 11.30% | 5.00% | 36.58% | 47.10% | NA |
| Indica Intermediate | 786 | 10.80% | 3.40% | 35.24% | 50.38% | T: 0.13% |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 65.90% | 0.00% | 3.77% | 30.36% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.00% | 1.24% | 12.86% | NA |
| VI/Aromatic | 96 | 86.50% | 2.10% | 4.17% | 7.29% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 15.56% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761624 | TGTTGGAAA -> T | LOC_Os03g31190.1 | frameshift_variant ; p.Phe146fs; HIGH | frameshift_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761624 | TGTTGGAAA -> TTATAGTTGGAAA | LOC_Os03g31190.1 | frameshift_variant ; p.Val149fs; HIGH | frameshift_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761624 | TGTTGGAAA -> TTATAGATCACTCGTTGGAAA | LOC_Os03g31190.1 | stop_gained&disruptive_inframe_insertion ; p.Thr148_Val149insSerAspLeuTer; HIGH | inframe_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761624 | TGTTGGAAA -> TTGTAGATCACTCGTTGGAAA | LOC_Os03g31190.1 | disruptive_inframe_insertion ; p.Thr148_Val149insSerAspLeuGln; MODERATE | inframe_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761624 | TGTTGGAAA -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |