12 variations found. Os12g0109633/LOC_Os12g01890 (SAG20; putative; expressed), ranging from 521,226 bp to 522,682 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g01890 | SAG20, putative; RAP ID: Os12g0109633; MSU ID: LOC_Os12g01890 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200521280 (J) | chr12 | 521280 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os12g01890.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os12g01880.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01900.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.756; most accessible tissue: Zhenshan97 flower, score: 83.172 |
| vg1200521290 (J) | chr12 | 521290 | A | C | 95.00% | 0.00% | A -> C | NA |
LOC_Os12g01890.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 65.315; most accessible tissue: Zhenshan97 flower, score: 84.018 |
| vg1200521307 (J) | chr12 | 521307 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os12g01890.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g01880.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.088; most accessible tissue: Zhenshan97 flower, score: 84.964 |
| vg1200521336 (J) | chr12 | 521336 | GCCT | GCCTCCT | 89.70% | 0.00% | GCCT -> GCCTCCT,G | NA |
LOC_Os12g01890.1 Alt: GCCTCCT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g01890.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff) LOC_Os12g01880.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.119; most accessible tissue: Zhenshan97 flower, score: 84.964 |
| vg1200521680 (J) | chr12 | 521680 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g01880.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g01900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01890.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.082; most accessible tissue: Zhenshan97 flower, score: 87.172 |
| vg1200521827 (J) | chr12 | 521827 | C | T | 71.50% | 0.00% | C -> T |
Grain_length (All); LR P-value: 3.13E-15;
Grain_length (Ind_All); LR P-value: 2.61E-16; mr1174 (All); LR P-value: 3.01E-08; mr1174_2 (All); LR P-value: 3.78E-09 |
LOC_Os12g01890.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.856; most accessible tissue: Zhenshan97 flower, score: 86.118 |
| vg1200521899 (J) | chr12 | 521899 | T | TCTC | 93.50% | 0.00% | T -> TCTC | NA |
LOC_Os12g01890.1 Alt: TCTC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 65.914; most accessible tissue: Zhenshan97 flower, score: 84.783 |
| vg1200522149 (J) | chr12 | 522149 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os12g01890.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.594; most accessible tissue: Zhenshan97 flower, score: 85.482 |
| vg1200522212 (J) | chr12 | 522212 | G | A | 90.40% | 0.00% | G -> A |
LOC_Os12g01890.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.426; most accessible tissue: Zhenshan97 flower, score: 81.855 |
|
| vg1200522479 (J) | chr12 | 522479 | C | T | 95.00% | 0.00% | C -> T | NA |
LOC_Os12g01890.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.614; most accessible tissue: Zhenshan97 root, score: 83.907 |
| vg1200522551 (J) | chr12 | 522551 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os12g01890.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g01900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.504; most accessible tissue: Zhenshan97 root, score: 86.140 |
| STR1200521901 (J) | chr12 | 521901 | T | TCGT | 94.80% | 0.00% | T -> TCGT | NA |
|