117 variations found. LOC_Os01g25760 (powdery mildew resistance protein PM3F; putative; expressed), ranging from 14,597,789 bp to 14,602,976 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114597892 (J) | chr01 | 14597892 | CA | C | 42.20% | 17.46% | CA -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.492; most accessible tissue: Zhenshan97 flower, score: 78.677 |
| vg0114598091 (J) | chr01 | 14598091 | C | A | 74.50% | 16.76% | C -> A | NA |
LOC_Os01g25760.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.807; most accessible tissue: Zhenshan97 flower, score: 83.605 |
| vg0114598124 (J) | chr01 | 14598124 | C | A | 75.40% | 16.78% | C -> A | NA |
LOC_Os01g25760.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.085; most accessible tissue: Zhenshan97 flower, score: 81.984 |
| vg0114598152 (J) | chr01 | 14598152 | A | ATACGGA G | 81.80% | 16.53% | A -> ATACGGAG | NA |
LOC_Os01g25760.1 Alt: ATACGGAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.793; most accessible tissue: Zhenshan97 flower, score: 81.047 |
| vg0114598332 (J) | chr01 | 14598332 | T | C | 41.90% | 17.67% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.669; most accessible tissue: Zhenshan97 flower, score: 79.365 |
| vg0114598359 (J) | chr01 | 14598359 | TAA | T | 83.00% | 16.27% | TAA -> T | NA |
LOC_Os01g25760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 66.108; most accessible tissue: Zhenshan97 root, score: 79.185 |
| vg0114598424 (J) | chr01 | 14598424 | G | C | 82.00% | 15.85% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.034; most accessible tissue: Zhenshan97 root, score: 74.466 |
| vg0114598481 (J) | chr01 | 14598481 | C | T | 62.40% | 17.33% | C -> T | NA |
LOC_Os01g25760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.867; most accessible tissue: Callus, score: 84.500 |
| vg0114598486 (J) | chr01 | 14598486 | G | T | 82.00% | 16.02% | G -> T | NA |
LOC_Os01g25760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.965; most accessible tissue: Callus, score: 84.500 |
| vg0114598571 (J) | chr01 | 14598571 | G | A | 41.90% | 17.86% | G -> A | NA |
LOC_Os01g25760.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.155; most accessible tissue: Callus, score: 84.500 |
| vg0114598620 (J) | chr01 | 14598620 | C | T | 42.30% | 17.48% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.852; most accessible tissue: Zhenshan97 root, score: 72.188 |
| vg0114598712 (J) | chr01 | 14598712 | T | C | 74.10% | 17.16% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.539; most accessible tissue: Callus, score: 83.537 |
| vg0114598728 (J) | chr01 | 14598728 | G | A | 82.90% | 16.48% | G -> A | NA |
LOC_Os01g25760.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.582; most accessible tissue: Callus, score: 83.537 |
| vg0114598743 (J) | chr01 | 14598743 | C | T | 82.40% | 16.61% | C -> T | NA |
LOC_Os01g25760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.128; most accessible tissue: Callus, score: 83.537 |
| vg0114598751 (J) | chr01 | 14598751 | CTTT | C | 83.00% | 16.38% | CTTT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.351; most accessible tissue: Callus, score: 83.537 |
| vg0114598931 (J) | chr01 | 14598931 | C | T | 82.60% | 16.19% | C -> T | NA |
LOC_Os01g25760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.603; most accessible tissue: Callus, score: 78.680 |
| vg0114599071 (J) | chr01 | 14599071 | T | G | 83.00% | 16.27% | T -> G | NA |
LOC_Os01g25760.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 64.490; most accessible tissue: Minghui63 flag leaf, score: 79.085 |
| vg0114599109 (J) | chr01 | 14599109 | C | G | 81.80% | 16.25% | C -> G | NA |
LOC_Os01g25760.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.313; most accessible tissue: Minghui63 flag leaf, score: 79.962 |
| vg0114599222 (J) | chr01 | 14599222 | G | C | 69.70% | 17.18% | G -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.777; most accessible tissue: Minghui63 flag leaf, score: 86.159 |
|
| vg0114599253 (J) | chr01 | 14599253 | G | A | 42.20% | 17.58% | A -> G | NA |
LOC_Os01g25760.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.830; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0114599274 (J) | chr01 | 14599274 | T | G | 82.70% | 9.84% | T -> G | NA |
LOC_Os01g25760.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.840; most accessible tissue: Zhenshan97 flower, score: 84.598 |
| vg0114599283 (J) | chr01 | 14599283 | C | G | 82.40% | 3.41% | C -> G | NA |
LOC_Os01g25760.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.743; most accessible tissue: Zhenshan97 flower, score: 84.692 |
| vg0114599299 (J) | chr01 | 14599299 | A | T | 82.40% | 3.17% | A -> T | NA |
LOC_Os01g25760.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.558; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0114599307 (J) | chr01 | 14599307 | G | A | 82.50% | 3.22% | G -> A | NA |
LOC_Os01g25760.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.915; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0114599314 (J) | chr01 | 14599314 | G | A | 82.40% | 3.17% | G -> A | NA |
LOC_Os01g25760.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g25760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.045; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
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