39 variations found. LOC_Os12g22430 (retrotransposon protein; putative; unclassified), ranging from 12,665,535 bp to 12,666,468 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666112 (J) | chr12 | 12666112 | G | A | 38.90% | 40.44% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666117 (J) | chr12 | 12666117 | A | G | 16.80% | 65.62% | A -> G | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666160 (J) | chr12 | 12666160 | G | A | 36.10% | 44.14% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666172 (J) | chr12 | 12666172 | C | T | 16.50% | 67.20% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666216 (J) | chr12 | 12666216 | G | C | 18.90% | 55.04% | G -> C | NA |
LOC_Os12g22430.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666243 (J) | chr12 | 12666243 | T | A | 50.50% | 36.99% | T -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666253 (J) | chr12 | 12666253 | G | A | 71.60% | 21.20% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666268 (J) | chr12 | 12666268 | C | T | 78.80% | 19.02% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666270 (J) | chr12 | 12666270 | G | A | 79.50% | 18.90% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666273 (J) | chr12 | 12666273 | G | A | 78.30% | 18.71% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666278 (J) | chr12 | 12666278 | G | A | 76.30% | 19.13% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666282 (J) | chr12 | 12666282 | C | T | 79.80% | 18.18% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666283 (J) | chr12 | 12666283 | A | G | 79.00% | 18.39% | A -> G | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666286 (J) | chr12 | 12666286 | C | T | 80.30% | 17.16% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666287 (J) | chr12 | 12666287 | C | A | 78.30% | 17.31% | C -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666289 (J) | chr12 | 12666289 | C | T | 81.50% | 16.72% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 4.447; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1212666291 (J) | chr12 | 12666291 | C | T | 81.70% | 16.69% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666304 (J) | chr12 | 12666304 | T | C | 81.70% | 16.65% | T -> C | NA |
LOC_Os12g22430.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666305 (J) | chr12 | 12666305 | C | T | 81.70% | 16.76% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666308 (J) | chr12 | 12666308 | C | T | 81.60% | 17.10% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666312 (J) | chr12 | 12666312 | C | T | 55.50% | 17.69% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666313 (J) | chr12 | 12666313 | G | A | 81.70% | 17.22% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666314 (J) | chr12 | 12666314 | C | T | 80.90% | 17.54% | C -> T,A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666317 (J) | chr12 | 12666317 | G | A | 81.70% | 17.18% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666329 (J) | chr12 | 12666329 | C | T | 81.50% | 17.27% | C -> T,CGCG | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: CGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666330 (J) | chr12 | 12666330 | G | C | 78.50% | 17.25% | G -> C | NA |
LOC_Os12g22430.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666331 (J) | chr12 | 12666331 | C | CAG | 81.70% | 17.20% | C -> CAG | NA |
LOC_Os12g22430.1 Alt: CAG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666332 (J) | chr12 | 12666332 | A | G | 81.10% | 17.22% | A -> G | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666333 (J) | chr12 | 12666333 | ACT | GCT | 80.90% | 17.20% | ACT -> GCT,A | NA |
LOC_Os12g22430.1 Alt: GCT| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g22430.1 Alt: GCT| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os12g22430.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666335 (J) | chr12 | 12666335 | C | T | 39.10% | 13.20% | T -> C,A | NA |
LOC_Os12g22430.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666370 (J) | chr12 | 12666370 | A | AATG | 20.50% | 57.93% | A -> AATG | NA |
LOC_Os12g22430.1 Alt: AATG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666373 (J) | chr12 | 12666373 | GAAAGTA | G | 17.90% | 58.72% | GAAAGTA -> G | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666377 (J) | chr12 | 12666377 | G | T | 16.90% | 63.14% | G -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666378 (J) | chr12 | 12666378 | T | A | 16.70% | 67.84% | T -> A,C | NA |
LOC_Os12g22430.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666385 (J) | chr12 | 12666385 | G | A | 30.50% | 55.18% | G -> A | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666387 (J) | chr12 | 12666387 | A | T | 16.30% | 70.59% | A -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g22430.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666409 (J) | chr12 | 12666409 | C | T | 16.50% | 65.34% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666415 (J) | chr12 | 12666415 | C | T | 16.50% | 65.91% | C -> T | NA |
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1212666466 (J) | chr12 | 12666466 | T | C | 16.70% | 65.72% | T -> C |
LOC_Os12g22430.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os12g22430.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.769; most accessible tissue: Zhenshan97 panicle, score: 16.188 |