22 variations found. LOC_Os03g32526 (tRNA-splicing endonuclease positive effector-related; putative; expressed), ranging from 18,602,726 bp to 18,608,700 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0318603416 (J) | chr03 | 18603416 | T | C | 97.20% | 2.22% | T -> C | NA |
LOC_Os03g32526.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0318603436 (J) | chr03 | 18603436 | A | G | 97.10% | 2.31% | A -> G | NA |
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g32526.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0318604245 (J) | chr03 | 18604245 | G | GTGATAT GACA | 95.90% | 2.69% | G -> GTGATATGAC A | NA |
LOC_Os03g32526.1 Alt: GTGATATGACA/frameshift_variant(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.820; most accessible tissue: Callus, score: 8.348 |
| vg0318604727 (J) | chr03 | 18604727 | C | CAG | 72.30% | 5.78% | C -> CAG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: CAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 14.260; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg0318607864 (J) | chr03 | 18607864 | T | C | 85.10% | 2.75% | T -> C | NA |
LOC_Os03g32540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0318607903 (J) | chr03 | 18607903 | A | C | 82.40% | 6.88% | A -> C | NA |
LOC_Os03g32540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0318608191 (J) | chr03 | 18608191 | T | C | 34.50% | 31.17% | T -> C | NA |
LOC_Os03g32526.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.950; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0318608236 (J) | chr03 | 18608236 | AACACAC ACAC | AAC | 51.70% | 0.08% | AACACACACA C -> AAC,AACACA C,AACACACA C,AACAC,A | NA |
LOC_Os03g32540.1 Alt: AACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: AACAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32540.1 Alt: AACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32526.1 Alt: AACACACAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g32540.1 Alt: AAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32526.1 Alt: AAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32526.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32540.1 Alt: AACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32526.1 Alt: AACACAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 |
| vg0318608283 (J) | chr03 | 18608283 | G | A | 92.00% | 0.04% | G -> A,T | NA |
LOC_Os03g32540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g32526.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 |
| vg0318608296 (J) | chr03 | 18608296 | G | A | 84.70% | 0.61% | G -> A | NA |
LOC_Os03g32540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 |
| vg0318608317 (J) | chr03 | 18608317 | C | A | 96.10% | 0.53% | C -> A | NA |
LOC_Os03g32526.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g32540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.400; most accessible tissue: Zhenshan97 panicle, score: 43.098 |
| vg0318608541 (J) | chr03 | 18608541 | G | A | 76.40% | 14.47% | G -> A | NA |
LOC_Os03g32540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g32526.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 31.763; most accessible tissue: Minghui63 young leaf, score: 61.007 |
| vg0318608574 (J) | chr03 | 18608574 | C | T | 58.30% | 20.31% | C -> T | NA |
LOC_Os03g32526.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.686; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608583 (J) | chr03 | 18608583 | C | A | 88.20% | 2.54% | C -> A | NA |
LOC_Os03g32526.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.562; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608601 (J) | chr03 | 18608601 | C | Unkown | 99.40% | 0.38% | C -> T | NA |
LOC_Os03g32526.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g32540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 31.565; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608620 (J) | chr03 | 18608620 | C | T | 99.30% | 0.38% | C -> T | NA |
LOC_Os03g32526.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.851; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608640 (J) | chr03 | 18608640 | C | G | 99.30% | 0.38% | C -> G,T | NA |
LOC_Os03g32526.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g32526.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 32.006; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608644 (J) | chr03 | 18608644 | CGAG | GGAG | 98.90% | 0.38% | CGAG -> GGAG,C | NA |
LOC_Os03g32526.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g32526.1 Alt: GGAG| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 31.487; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0318608662 (J) | chr03 | 18608662 | GC | G | 99.30% | 0.13% | GC -> G | NA |
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g32526.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 32.259; most accessible tissue: Minghui63 young leaf, score: 64.378 |
| vg0318608665 (J) | chr03 | 18608665 | TCCGCCT CC | T | 98.80% | 0.51% | TCCGCCTCC -> T | NA |
LOC_Os03g32526.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.653; most accessible tissue: Minghui63 young leaf, score: 64.378 |
| vg0318608678 (J) | chr03 | 18608678 | C | Unkown | 99.40% | 0.21% | C -> T,G | NA |
LOC_Os03g32526.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g32540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g32526.1 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g32540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 32.741; most accessible tissue: Minghui63 young leaf, score: 65.920 |
| vg0318608683 (J) | chr03 | 18608683 | G | A | 96.30% | 0.57% | G -> A | NA |
LOC_Os03g32526.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g32526.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.741; most accessible tissue: Minghui63 young leaf, score: 65.920 |