15 variations found. LOC_Os04g23880 (transposon protein; putative; unclassified; expressed), ranging from 13,635,827 bp to 13,639,063 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0413636905 (J) | chr04 | 13636905 | C | T | 30.40% | 64.28% | C -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0413637169 (J) | chr04 | 13637169 | T | C | 30.30% | 61.64% | T -> C | NA |
LOC_Os04g23880.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.341; most accessible tissue: Zhenshan97 flower, score: 17.420 |
| vg0413637238 (J) | chr04 | 13637238 | G | A | 30.50% | 60.60% | G -> A | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 12.815; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 |
| vg0413638055 (J) | chr04 | 13638055 | C | T | 30.80% | 63.84% | C -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.991; most accessible tissue: Callus, score: 10.231 |
| vg0413638158 (J) | chr04 | 13638158 | G | A | 33.80% | 61.91% | G -> A | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.994; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0413638176 (J) | chr04 | 13638176 | T | A | 33.70% | 61.89% | T -> A | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.631; most accessible tissue: Callus, score: 9.730 |
| vg0413638197 (J) | chr04 | 13638197 | A | G | 31.60% | 66.78% | A -> G | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.708; most accessible tissue: Zhenshan97 young leaf, score: 10.013 |
| vg0413638413 (J) | chr04 | 13638413 | C | T | 32.00% | 65.15% | C -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.722; most accessible tissue: Zhenshan97 young leaf, score: 11.658 |
| vg0413638470 (J) | chr04 | 13638470 | G | A | 31.20% | 67.86% | G -> A | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.860; most accessible tissue: Zhenshan97 young leaf, score: 11.658 |
| vg0413638509 (J) | chr04 | 13638509 | A | G | 31.40% | 66.42% | A -> G | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.860; most accessible tissue: Zhenshan97 young leaf, score: 11.658 |
| vg0413638548 (J) | chr04 | 13638548 | C | T | 31.80% | 67.14% | C -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.711; most accessible tissue: Zhenshan97 young leaf, score: 10.013 |
| vg0413638560 (J) | chr04 | 13638560 | G | Unkown | 33.50% | 63.39% | G -> A | NA |
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os04g23870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g23890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g23890.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g23890.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g23890.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 5.554; most accessible tissue: Callus, score: 9.758 |
| vg0413638572 (J) | chr04 | 13638572 | G | A | 31.60% | 67.25% | G -> A | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.475; most accessible tissue: Callus, score: 9.758 |
| vg0413638632 (J) | chr04 | 13638632 | C | T | 29.90% | 67.08% | C -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.822; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0413638881 (J) | chr04 | 13638881 | G | T | 31.60% | 65.68% | G -> T | NA |
LOC_Os04g23880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g23880.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |