32 variations found. LOC_Os11g40920 (retrotransposon protein; putative; unclassified; expressed), ranging from 24,490,249 bp to 24,499,759 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124490758 (J) | chr11 | 24490758 | G | A | 44.90% | 46.47% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.525; most accessible tissue: Zhenshan97 flower, score: 19.041 |
| vg1124490801 (J) | chr11 | 24490801 | G | A | 40.70% | 46.47% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.525; most accessible tissue: Zhenshan97 flower, score: 19.041 |
| vg1124491135 (J) | chr11 | 24491135 | C | T | 28.80% | 49.47% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124491295 (J) | chr11 | 24491295 | G | A | 41.80% | 53.64% | G -> A | NA |
LOC_Os11g40900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g40910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124494077 (J) | chr11 | 24494077 | G | A | 31.40% | 54.87% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124494138 (J) | chr11 | 24494138 | CT | CTT | 46.40% | 52.12% | CT -> CTT,C | NA |
LOC_Os11g40920.1 Alt: CTT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g40920.1 Alt: C| frameshift_variant HIGH(snpEff) LOC_Os11g40910.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124494450 (J) | chr11 | 24494450 | C | T | 37.90% | 55.54% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494517 (J) | chr11 | 24494517 | T | A | 46.70% | 51.35% | T -> A | NA |
LOC_Os11g40920.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494529 (J) | chr11 | 24494529 | A | T | 46.50% | 52.03% | A -> T | NA |
LOC_Os11g40920.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494532 (J) | chr11 | 24494532 | A | G | 46.50% | 52.03% | A -> G | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494544 (J) | chr11 | 24494544 | A | G | 46.40% | 52.09% | A -> G | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494548 (J) | chr11 | 24494548 | C | T | 46.40% | 52.12% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494555 (J) | chr11 | 24494555 | A | G | 46.30% | 52.20% | A -> G | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494556 (J) | chr11 | 24494556 | T | C | 46.30% | 52.22% | T -> C | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494559 (J) | chr11 | 24494559 | G | A | 46.30% | 52.22% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494562 (J) | chr11 | 24494562 | A | G | 46.30% | 52.22% | A -> G | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124494571 (J) | chr11 | 24494571 | C | A | 46.20% | 52.26% | C -> A | NA |
LOC_Os11g40920.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.735; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1124496159 (J) | chr11 | 24496159 | T | C | 21.60% | 54.15% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124496243 (J) | chr11 | 24496243 | G | A | 44.50% | 54.06% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.460; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124496610 (J) | chr11 | 24496610 | G | A | 45.30% | 52.01% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.975; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg1124497004 (J) | chr11 | 24497004 | G | C | 42.10% | 53.89% | G -> C | NA |
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g40920.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.242; most accessible tissue: Callus, score: 12.988 |
| vg1124497175 (J) | chr11 | 24497175 | C | T | 33.90% | 61.17% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g40920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.477; most accessible tissue: Callus, score: 15.581 |
| vg1124497721 (J) | chr11 | 24497721 | G | T | 47.00% | 50.70% | G -> T | NA |
LOC_Os11g40920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.384; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1124497775 (J) | chr11 | 24497775 | C | T | 18.00% | 63.01% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.384; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1124497925 (J) | chr11 | 24497925 | C | T | 6.30% | 86.12% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.887; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg1124498033 (J) | chr11 | 24498033 | G | A | 3.30% | 76.72% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.974; most accessible tissue: Callus, score: 10.045 |
| vg1124498071 (J) | chr11 | 24498071 | T | A | 44.00% | 51.29% | T -> A | NA |
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.974; most accessible tissue: Callus, score: 10.045 |
| vg1124498078 (J) | chr11 | 24498078 | C | T | 44.80% | 51.71% | C -> T | NA |
LOC_Os11g40920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.481; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124498929 (J) | chr11 | 24498929 | G | A | 44.30% | 54.13% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.445; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1124498958 (J) | chr11 | 24498958 | G | A | 44.10% | 54.06% | G -> A | NA |
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.471; most accessible tissue: Zhenshan97 root, score: 18.731 |
| vg1124499281 (J) | chr11 | 24499281 | T | A | 37.10% | 55.48% | T -> A | NA |
LOC_Os11g40930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 18.599; most accessible tissue: Zhenshan97 root, score: 58.674 |
| vg1124499364 (J) | chr11 | 24499364 | G | A | 44.90% | 53.77% | G -> A | NA |
LOC_Os11g40930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g40920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 17.318; most accessible tissue: Zhenshan97 root, score: 53.045 |