21 variations found. LOC_Os05g20520 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 12,045,111 bp to 12,047,043 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045211 (J) | chr05 | 12045211 | C | T | 82.70% | 10.45% | C -> T | NA |
LOC_Os05g20520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 26.118; most accessible tissue: Zhenshan97 young leaf, score: 43.230 |
| vg0512045241 (J) | chr05 | 12045241 | C | A | 83.20% | 11.38% | C -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 23.740; most accessible tissue: Zhenshan97 young leaf, score: 34.553 |
| vg0512045274 (J) | chr05 | 12045274 | C | G | 84.50% | 11.07% | C -> G | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 23.186; most accessible tissue: Minghui63 young leaf, score: 32.638 |
| vg0512045288 (J) | chr05 | 12045288 | C | A | 84.70% | 11.05% | C -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 22.474; most accessible tissue: Minghui63 young leaf, score: 32.638 |
| vg0512045340 (J) | chr05 | 12045340 | A | G | 82.40% | 11.36% | A -> G | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 18.155; most accessible tissue: Minghui63 young leaf, score: 24.836 |
| vg0512045352 (J) | chr05 | 12045352 | G | A | 86.40% | 10.05% | G -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 17.315; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045386 (J) | chr05 | 12045386 | G | A | 82.20% | 9.99% | G -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 16.235; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045434 (J) | chr05 | 12045434 | T | C | 82.10% | 10.05% | T -> C | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 15.294; most accessible tissue: Zhenshan97 flower, score: 25.980 |
| vg0512045441 (J) | chr05 | 12045441 | G | A | 84.00% | 11.66% | G -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 15.236; most accessible tissue: Zhenshan97 flower, score: 25.980 |
| vg0512045460 (J) | chr05 | 12045460 | T | C | 82.10% | 11.28% | T -> C | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 12.233; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045463 (J) | chr05 | 12045463 | A | G | 82.10% | 11.30% | A -> G | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.949; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045466 (J) | chr05 | 12045466 | G | T | 82.10% | 11.62% | G -> T | NA |
LOC_Os05g20520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.949; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045481 (J) | chr05 | 12045481 | C | T | 82.10% | 12.61% | C -> T | NA |
LOC_Os05g20520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045482 (J) | chr05 | 12045482 | G | A | 85.10% | 11.26% | G -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045484 (J) | chr05 | 12045484 | A | G | 82.10% | 12.51% | A -> G | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 |
| vg0512045572 (J) | chr05 | 12045572 | C | T | 84.30% | 12.29% | C -> T | NA |
LOC_Os05g20520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.384; most accessible tissue: Zhenshan97 flower, score: 19.041 |
| vg0512045644 (J) | chr05 | 12045644 | C | T | 85.60% | 9.94% | C -> T | NA |
LOC_Os05g20520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.575; most accessible tissue: Zhenshan97 flower, score: 17.420 |
| vg0512046474 (J) | chr05 | 12046474 | C | G | 87.20% | 9.50% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g20510.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g20520.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.787; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0512046495 (J) | chr05 | 12046495 | A | G | 87.10% | 10.09% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g20510.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g20520.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 21.217; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 |
| vg0512046885 (J) | chr05 | 12046885 | C | A | 82.50% | 9.61% | C -> A | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 36.021; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0512046891 (J) | chr05 | 12046891 | T | C | 84.10% | 9.67% | T -> C | NA |
LOC_Os05g20520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20520.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 37.370; most accessible tissue: Zhenshan97 panicle, score: 68.538 |