32 variations found. LOC_Os11g09660 (retrotransposon protein; putative; unclassified; expressed), ranging from 5,159,722 bp to 5,161,120 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159758 (J) | chr11 | 5159758 | C | T | 33.60% | 45.87% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.323; most accessible tissue: Callus, score: 10.907 |
| vg1105159777 (J) | chr11 | 5159777 | G | A | 40.80% | 33.81% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.323; most accessible tissue: Callus, score: 10.907 |
| vg1105159795 (J) | chr11 | 5159795 | G | A | 41.30% | 34.77% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.323; most accessible tissue: Callus, score: 10.907 |
| vg1105159831 (J) | chr11 | 5159831 | T | C | 48.70% | 33.69% | T -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.072; most accessible tissue: Callus, score: 8.148 |
| vg1105159835 (J) | chr11 | 5159835 | C | T | 56.60% | 32.99% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.072; most accessible tissue: Callus, score: 8.148 |
| vg1105159860 (J) | chr11 | 5159860 | G | A | 55.00% | 33.31% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.462; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg1105159876 (J) | chr11 | 5159876 | A | G | 32.20% | 50.15% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg1105159886 (J) | chr11 | 5159886 | G | A | 22.10% | 60.14% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg1105159978 (J) | chr11 | 5159978 | G | A | 27.40% | 48.10% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.360; most accessible tissue: Callus, score: 13.429 |
| vg1105159988 (J) | chr11 | 5159988 | G | A | 12.80% | 67.99% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.360; most accessible tissue: Callus, score: 13.429 |
| vg1105160032 (J) | chr11 | 5160032 | A | AC | 22.20% | 63.27% | AC -> A | NA |
LOC_Os11g09660.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.360; most accessible tissue: Callus, score: 13.429 |
| vg1105160088 (J) | chr11 | 5160088 | A | G | 10.70% | 71.07% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 |
| vg1105160158 (J) | chr11 | 5160158 | C | T | 40.30% | 35.57% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 |
| vg1105160339 (J) | chr11 | 5160339 | C | T | 9.90% | 65.28% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.966; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160440 (J) | chr11 | 5160440 | G | A | 10.50% | 62.15% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160500 (J) | chr11 | 5160500 | G | T | 10.70% | 62.04% | G -> T | NA |
LOC_Os11g09660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160507 (J) | chr11 | 5160507 | T | G | 13.20% | 61.68% | T -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160525 (J) | chr11 | 5160525 | G | A | 10.70% | 70.10% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160867 (J) | chr11 | 5160867 | G | A | 33.50% | 51.78% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160887 (J) | chr11 | 5160887 | G | C | 33.50% | 50.76% | G -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160997 (J) | chr11 | 5160997 | C | T | 64.00% | 26.60% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105160999 (J) | chr11 | 5160999 | T | C | 48.90% | 32.16% | T -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105161001 (J) | chr11 | 5161001 | C | T | 64.30% | 27.32% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105161006 (J) | chr11 | 5161006 | T | G | 60.50% | 25.41% | T -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105161011 (J) | chr11 | 5161011 | C | T | 74.90% | 15.89% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg1105161038 (J) | chr11 | 5161038 | C | T | 83.00% | 14.43% | C -> T | NA |
LOC_Os11g09660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.942; most accessible tissue: Callus, score: 11.873 |
| vg1105161058 (J) | chr11 | 5161058 | T | C | 43.40% | 12.63% | T -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.031; most accessible tissue: Callus, score: 11.873 |
| vg1105161067 (J) | chr11 | 5161067 | G | A | 83.10% | 14.64% | G -> A | NA |
LOC_Os11g09660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.942; most accessible tissue: Callus, score: 11.873 |
| vg1105161082 (J) | chr11 | 5161082 | A | G | 40.50% | 13.39% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.487; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg1105161095 (J) | chr11 | 5161095 | T | C | 83.10% | 14.68% | T -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.020; most accessible tissue: Minghui63 root, score: 10.708 |
| vg1105161113 (J) | chr11 | 5161113 | T | C | 34.20% | 16.25% | T -> C | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.249; most accessible tissue: Minghui63 root, score: 13.235 |
| vg1105161115 (J) | chr11 | 5161115 | A | G | 33.60% | 16.38% | A -> G | NA |
LOC_Os11g09660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.249; most accessible tissue: Minghui63 root, score: 13.235 |