26 variations found. LOC_Os04g26690 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 15,571,113 bp to 15,576,369 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0415572547 (J) | chr04 | 15572547 | G | Unkown | 71.50% | 21.67% | G -> A | NA |
LOC_Os04g26690.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g26670.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g26680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.422; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0415573913 (J) | chr04 | 15573913 | T | C | 0.30% | 58.97% | C -> T | NA |
LOC_Os04g26690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g26690.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.210; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0415573926 (J) | chr04 | 15573926 | G | T | 0.20% | 57.96% | T -> G | NA |
LOC_Os04g26690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g26690.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 9.228; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0415575320 (J) | chr04 | 15575320 | G | A | 71.00% | 21.86% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.603; most accessible tissue: Zhenshan97 flower, score: 18.233 |
| vg0415575382 (J) | chr04 | 15575382 | T | C | 77.40% | 19.11% | T -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.916; most accessible tissue: Zhenshan97 flower, score: 18.233 |
| vg0415575609 (J) | chr04 | 15575609 | C | T | 77.90% | 20.31% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 31.224; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 |
| vg0415575620 (J) | chr04 | 15575620 | C | A | 71.10% | 21.75% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.198; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 |
| vg0415575690 (J) | chr04 | 15575690 | TCCTCCT CCCCCTC CGCCACC TCCACTA | T | 66.40% | 20.69% | TCCTCCTCCC CCTCCGCCAC CTCCACTA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.066; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 |
| vg0415575704 (J) | chr04 | 15575704 | C | T | 70.90% | 22.01% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.322; most accessible tissue: Zhenshan97 young leaf, score: 59.009 |
| vg0415575708 (J) | chr04 | 15575708 | T | A | 61.60% | 23.00% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.567; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 |
| vg0415575714 (J) | chr04 | 15575714 | C | A | 60.70% | 23.32% | A -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 40.858; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 |
| vg0415575717 (J) | chr04 | 15575717 | T | A | 60.40% | 23.40% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.430; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 |
| vg0415575752 (J) | chr04 | 15575752 | CCATCCC CGG | C | 79.80% | 17.60% | CCATCCCCGG -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 |
| vg0415575753 (J) | chr04 | 15575753 | CATCCCC GGCCCTC T | C | 79.60% | 17.60% | CATCCCCGGC CCTCT -> C,CCCCCGGC CCTCT | NA |
LOC_Os04g26690.1 Alt: CCCCCGGCCCTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 |
| vg0415575757 (J) | chr04 | 15575757 | C | A | 79.50% | 17.99% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 |
| vg0415575759 (J) | chr04 | 15575759 | C | T | 77.40% | 20.17% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 |
| vg0415575776 (J) | chr04 | 15575776 | T | A | 77.70% | 20.95% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.600; most accessible tissue: Zhenshan97 young leaf, score: 65.804 |
| vg0415575789 (J) | chr04 | 15575789 | T | TC | 77.50% | 20.95% | T -> TC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.830 |
| vg0415575791 (J) | chr04 | 15575791 | G | A | 77.40% | 21.22% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.830 |
| vg0415575794 (J) | chr04 | 15575794 | C | T | 77.40% | 20.84% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.830 |
| vg0415575796 (J) | chr04 | 15575796 | G | A | 78.00% | 21.12% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.830 |
| vg0415575861 (J) | chr04 | 15575861 | C | T | 70.80% | 22.09% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.652; most accessible tissue: Zhenshan97 young leaf, score: 62.534 |
| vg0415575876 (J) | chr04 | 15575876 | A | C | 70.40% | 22.24% | A -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 41.653; most accessible tissue: Zhenshan97 young leaf, score: 61.964 |
| vg0415575918 (J) | chr04 | 15575918 | T | C | 69.80% | 22.77% | T -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 39.734; most accessible tissue: Zhenshan97 young leaf, score: 60.800 |
| vg0415575989 (J) | chr04 | 15575989 | CT | C | 33.80% | 26.81% | CT -> C | NA |
LOC_Os04g26690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 29.657; most accessible tissue: Zhenshan97 young leaf, score: 47.986 |
| vg0415576085 (J) | chr04 | 15576085 | G | A | 63.20% | 23.38% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g26690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.424; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 |