18 variations found. Os10g0131500/LOC_Os10g04160 (expressed protein), ranging from 1,932,696 bp to 1,933,882 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os10g04160 | hypothetical protein; RAP ID: Os10g0131500; MSU ID: LOC_Os10g04160 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001932741 (J) | chr10 | 1932741 | C | A | 84.90% | 13.97% | C -> A | NA |
LOC_Os10g04160.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 33.896; most accessible tissue: Callus, score: 65.274 |
| vg1001932749 (J) | chr10 | 1932749 | T | C | 50.90% | 15.70% | T -> C | NA |
LOC_Os10g04160.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.343; most accessible tissue: Callus, score: 65.274 |
| vg1001932853 (J) | chr10 | 1932853 | C | G | 84.90% | 14.18% | C -> G | NA |
LOC_Os10g04140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g04150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g04160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 32.203; most accessible tissue: Zhenshan97 young leaf, score: 63.653 |
| vg1001933010 (J) | chr10 | 1933010 | CTG | GTG | 43.00% | 16.10% | CTG -> GTG,TTG,C | NA |
LOC_Os10g04160.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g04160.1 Alt: TTG| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os10g04160.1 Alt: GTG| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 36.773; most accessible tissue: Callus, score: 73.936 |
| vg1001933049 (J) | chr10 | 1933049 | T | G | 80.10% | 15.23% | T -> G | NA |
LOC_Os10g04160.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.805; most accessible tissue: Callus, score: 73.936 |
| vg1001933162 (J) | chr10 | 1933162 | A | T | 81.50% | 14.81% | A -> T | NA |
LOC_Os10g04160.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 41.396; most accessible tissue: Zhenshan97 young leaf, score: 75.039 |
| vg1001933229 (J) | chr10 | 1933229 | C | T | 84.90% | 14.56% | C -> T | NA |
LOC_Os10g04160.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.828; most accessible tissue: Callus, score: 77.054 |
| vg1001933300 (J) | chr10 | 1933300 | C | G | 84.70% | 14.79% | C -> G | NA |
LOC_Os10g04160.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 41.288; most accessible tissue: Callus, score: 77.054 |
| vg1001933309 (J) | chr10 | 1933309 | C | A | 84.70% | 14.47% | C -> A | NA |
LOC_Os10g04160.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.867; most accessible tissue: Callus, score: 77.054 |
| vg1001933318 (J) | chr10 | 1933318 | C | T | 84.70% | 14.56% | C -> T | NA |
LOC_Os10g04160.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.827; most accessible tissue: Callus, score: 77.054 |
| vg1001933464 (J) | chr10 | 1933464 | A | G | 84.20% | 14.79% | A -> G | NA |
LOC_Os10g04160.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.007; most accessible tissue: Callus, score: 75.859 |
| vg1001933465 (J) | chr10 | 1933465 | T | C | 80.20% | 15.15% | T -> C | NA |
LOC_Os10g04160.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 39.946; most accessible tissue: Callus, score: 75.859 |
| vg1001933511 (J) | chr10 | 1933511 | GTATGAT | CTATGAT | 81.40% | 14.77% | GTATGAT -> CTATGAT,G | NA |
LOC_Os10g04160.1 Alt: CTATGAT| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g04160.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 39.167; most accessible tissue: Callus, score: 75.859 |
| vg1001933542 (J) | chr10 | 1933542 | T | TGGCTGA A | 84.10% | 14.77% | T -> TGGCTGAA | NA |
LOC_Os10g04160.1 Alt: TGGCTGAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 38.982; most accessible tissue: Callus, score: 75.859 |
| vg1001933571 (J) | chr10 | 1933571 | G | T | 84.20% | 14.73% | G -> T | NA |
LOC_Os10g04160.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 38.442; most accessible tissue: Callus, score: 75.859 |
| vg1001933710 (J) | chr10 | 1933710 | C | T | 81.40% | 14.77% | C -> T | NA |
LOC_Os10g04160.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 39.885; most accessible tissue: Minghui63 root, score: 74.461 |
| vg1001933837 (J) | chr10 | 1933837 | T | A | 81.40% | 14.83% | T -> A | NA |
LOC_Os10g04160.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.450; most accessible tissue: Minghui63 root, score: 66.549 |
| vg1001933839 (J) | chr10 | 1933839 | T | C | 47.10% | 16.12% | T -> C |
LOC_Os10g04160.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g04160.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.450; most accessible tissue: Minghui63 root, score: 66.549 |