12 variations found. Os12g0431700/LOC_Os12g24390 (retrotransposon protein; putative; unclassified; expressed), ranging from 13,913,931 bp to 13,915,732 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g24390 | retrotransposon protein, putative, unclassified, expressed; RAP ID: Os12g0431700; MSU ID: LOC_Os12g24390 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1213913940 (J) | chr12 | 13913940 | C | T | 90.00% | 0.00% | T -> C | NA |
LOC_Os12g24390.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.293; most accessible tissue: Zhenshan97 root, score: 90.979 |
| vg1213914027 (J) | chr12 | 13914027 | C | T | 50.00% | 0.00% | C -> T |
mr1190 (All); LR P-value: 1.76E-07;
mr1207 (All); LR P-value: 1.39E-06; mr1209 (All); LR P-value: 3.52E-06; mr1308 (Ind_All); LR P-value: 2.44E-06; mr1460 (All); LR P-value: 2.47E-06; mr1606 (Jap_All); LR P-value: 6.37E-06; mr1633 (All); LR P-value: 2.44E-06; mr1700 (Jap_All); LR P-value: 9.68E-06; mr1706 (All); LR P-value: 5.54E-08; mr1866 (All); LR P-value: 1.10E-08 |
LOC_Os12g24400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g24390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.171; most accessible tissue: Callus, score: 90.748 |
| vg1213914083 (J) | chr12 | 13914083 | A | AATAT | 87.00% | 0.34% | A -> AATAT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g24400.1 Alt: AATAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g24390.1 Alt: AATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.169; most accessible tissue: Zhenshan97 young leaf, score: 88.387 |
| vg1213914348 (J) | chr12 | 13914348 | C | T | 87.00% | 0.11% | C -> T | NA |
LOC_Os12g24390.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g24390.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 76.360; most accessible tissue: Zhenshan97 young leaf, score: 91.967 |
| vg1213914514 (J) | chr12 | 13914514 | G | A | 90.60% | 0.00% | G -> A |
LOC_Os12g24390.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.969; most accessible tissue: Zhenshan97 young leaf, score: 90.270 |
|
| vg1213914515 (J) | chr12 | 13914515 | T | C | 90.60% | 0.00% | T -> C |
LOC_Os12g24390.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.969; most accessible tissue: Zhenshan97 young leaf, score: 90.270 |
|
| vg1213914611 (J) | chr12 | 13914611 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os12g24390.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g24400.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.316; most accessible tissue: Zhenshan97 young leaf, score: 90.985 |
| vg1213914745 (J) | chr12 | 13914745 | G | A | 98.00% | 0.00% | G -> A | NA |
LOC_Os12g24400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g24390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.082; most accessible tissue: Zhenshan97 young leaf, score: 90.638 |
| vg1213914829 (J) | chr12 | 13914829 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os12g24390.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g24400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.010; most accessible tissue: Zhenshan97 young leaf, score: 89.875 |
| vg1213914838 (J) | chr12 | 13914838 | C | T | 87.10% | 0.02% | C -> T,G | NA |
LOC_Os12g24390.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g24390.1 Alt: G| synonymous_variant LOW(snpEff) LOC_Os12g24400.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g24390.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 76.947; most accessible tissue: Zhenshan97 young leaf, score: 89.559 |
| vg1213915024 (J) | chr12 | 13915024 | A | C | 99.30% | 0.00% | A -> C | NA |
LOC_Os12g24390.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os12g24400.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.076; most accessible tissue: Zhenshan97 young leaf, score: 91.389 |
| vg1213915685 (J) | chr12 | 13915685 | A | C | 52.60% | 0.00% | C -> A |
Grain_length (Ind_All); LR P-value: 1.60E-14;
mr1192 (Ind_All); LR P-value: 1.99E-06; mr1308 (Ind_All); LR P-value: 6.44E-06; mr1763 (Jap_All); LR P-value: 7.42E-06; mr1024_2 (Ind_All); LR P-value: 1.33E-06; mr1265_2 (All); LR P-value: 6.03E-06; mr1332_2 (All); LR P-value: 3.95E-07; mr1355_2 (All); LR P-value: 4.99E-06; mr1977_2 (All); LR P-value: 3.82E-07 |
LOC_Os12g24390.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 76.989; most accessible tissue: Zhenshan97 root, score: 91.642 |