25 variations found. LOC_Os07g42460 (transposon protein; putative; unclassified; expressed), ranging from 25,418,274 bp to 25,421,409 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725418494 (J) | chr07 | 25418494 | C | G | 21.10% | 73.89% | C -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.976; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0725419338 (J) | chr07 | 25419338 | G | A | 20.70% | 77.76% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42460.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.870; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0725420600 (J) | chr07 | 25420600 | C | T | 26.60% | 61.30% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.601; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0725421170 (J) | chr07 | 25421170 | A | G | 21.50% | 74.82% | A -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0725421179 (J) | chr07 | 25421179 | C | T | 25.20% | 71.29% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.012; most accessible tissue: Minghui63 root, score: 10.708 |
| vg0725421185 (J) | chr07 | 25421185 | G | A | 23.10% | 72.89% | G -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.633; most accessible tissue: Minghui63 root, score: 10.708 |
| vg0725421218 (J) | chr07 | 25421218 | A | G | 24.20% | 73.36% | A -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421224 (J) | chr07 | 25421224 | C | T | 27.70% | 70.72% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421227 (J) | chr07 | 25421227 | T | C | 24.80% | 73.21% | T -> C | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421242 (J) | chr07 | 25421242 | T | A | 26.90% | 71.39% | T -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421246 (J) | chr07 | 25421246 | A | G | 25.90% | 71.86% | A -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421247 (J) | chr07 | 25421247 | C | T | 24.30% | 73.64% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421252 (J) | chr07 | 25421252 | G | A | 24.30% | 73.59% | G -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421257 (J) | chr07 | 25421257 | C | T | 23.50% | 73.97% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421258 (J) | chr07 | 25421258 | A | G | 23.50% | 73.93% | A -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421273 (J) | chr07 | 25421273 | C | T | 26.30% | 71.22% | C -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421277 (J) | chr07 | 25421277 | G | C | 20.50% | 74.76% | G -> C | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421299 (J) | chr07 | 25421299 | G | A | 27.70% | 70.50% | G -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.770; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0725421320 (J) | chr07 | 25421320 | A | G | 22.30% | 74.02% | A -> G | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.941; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 |
| vg0725421347 (J) | chr07 | 25421347 | C | G | 24.40% | 73.85% | C -> G,T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g42460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |
| vg0725421356 (J) | chr07 | 25421356 | G | A | 25.00% | 70.84% | G -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |
| vg0725421359 (J) | chr07 | 25421359 | G | A | 24.80% | 73.74% | G -> A | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |
| vg0725421377 (J) | chr07 | 25421377 | A | C | 25.80% | 70.95% | A -> C | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |
| vg0725421381 (J) | chr07 | 25421381 | A | T | 23.70% | 74.27% | A -> T | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |
| vg0725421392 (J) | chr07 | 25421392 | T | C | 23.40% | 74.38% | T -> C | NA |
LOC_Os07g42460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.820; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 |