19 variations found. Os06g0205000/LOC_Os06g10340 (autophagy-related protein 12; putative; expressed), ranging from 5,308,991 bp to 5,310,602 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os06g10340 | autophagy-related protein 12, putative, expressed; RAP ID: Os06g0205000; MSU ID: LOC_Os06g10340 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os06g10340 | Os06g0205000 | OsATG12 | autophagy 12 | Q69NP0. | ATG12 | AUTOPHAGY ASSOCIATED GENE 12 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309168 (J) | chr06 | 5309168 | C | T | 89.40% | 0.00% | C -> T |
mr1201 (All); LMM P-value: 6.17E-21; LR P-value: 5.18E-39;
mr1201 (Ind_All); LMM P-value: 2.47E-19; LR P-value: 2.64E-41; mr1219 (All); LMM P-value: 3.34E-17; LR P-value: 5.28E-30; mr1219 (Ind_All); LMM P-value: 2.20E-17; LR P-value: 5.91E-37; mr1274 (All); LMM P-value: 1.77E-20; LR P-value: 9.85E-40; mr1274 (Ind_All); LMM P-value: 6.75E-20; LR P-value: 4.70E-37; mr1201_2 (All); LMM P-value: 5.82E-19; LR P-value: 1.88E-35; mr1201_2 (Ind_All); LMM P-value: 9.12E-19; LR P-value: 2.75E-36; mr1219_2 (All); LMM P-value: 3.28E-16; LR P-value: 2.52E-27; mr1219_2 (Ind_All); LMM P-value: 6.68E-17; LR P-value: 3.40E-33; mr1274_2 (All); LMM P-value: 2.95E-17; LR P-value: 5.34E-35; mr1274_2 (Ind_All); LMM P-value: 1.59E-17; LR P-value: 9.34E-36 |
LOC_Os06g10320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.261; most accessible tissue: Minghui63 young leaf, score: 92.670 |
| vg0605309419 (J) | chr06 | 5309419 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os06g10320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g10330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10340.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.202; most accessible tissue: Minghui63 panicle, score: 86.012 |
| vg0605309496 (J) | chr06 | 5309496 | GAA | G | 89.00% | 0.08% | GAA -> G | NA |
LOC_Os06g10320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.243; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0605309501 (J) | chr06 | 5309501 | AGGG | GGGG | 56.90% | 11.89% | AGGG -> GGGG,AG,A | NA |
LOC_Os06g10320.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: AG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os06g10320.1 Alt: GGGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10330.1 Alt: GGGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: GGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 |
| vg0605309504 (J) | chr06 | 5309504 | G | A | 48.50% | 10.71% | G -> A | NA |
LOC_Os06g10320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.067; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0605309508 (J) | chr06 | 5309508 | G | C | 93.50% | 1.59% | G -> C | NA |
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.246; most accessible tissue: Minghui63 young leaf, score: 82.907 |
| vg0605309574 (J) | chr06 | 5309574 | T | C | 86.90% | 0.00% | T -> C |
mr1201 (All); LMM P-value: 8.77E-23; LR P-value: 4.65E-42;
mr1201 (Ind_All); LMM P-value: 2.54E-20; LR P-value: 1.80E-42; mr1219 (All); LMM P-value: 7.00E-19; LR P-value: 3.38E-31; mr1219 (Ind_All); LMM P-value: 9.18E-18; LR P-value: 1.49E-37; mr1274 (All); LMM P-value: 1.23E-20; LR P-value: 4.11E-37; mr1274 (Ind_All); LMM P-value: 2.46E-22; LR P-value: 1.02E-38; mr1201_2 (All); LMM P-value: 1.89E-21; LR P-value: 1.79E-37; mr1201_2 (Ind_All); LMM P-value: 9.50E-20; LR P-value: 6.49E-37; mr1219_2 (All); LMM P-value: 1.33E-17; LR P-value: 1.66E-28; mr1219_2 (Ind_All); LMM P-value: 9.94E-18; LR P-value: 4.34E-34; mr1274_2 (All); LMM P-value: 2.00E-16; LR P-value: 1.79E-34; mr1274_2 (Ind_All); LMM P-value: 3.99E-18; LR P-value: 2.01E-36 |
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.303; most accessible tissue: Minghui63 panicle, score: 82.797 |
| vg0605309577 (J) | chr06 | 5309577 | ATAG | A | 86.80% | 0.36% | ATAG -> A | NA |
LOC_Os06g10320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 69.278; most accessible tissue: Minghui63 young leaf, score: 82.907 |
| vg0605309582 (J) | chr06 | 5309582 | AG | A | 98.10% | 0.00% | AG -> A | NA |
LOC_Os06g10320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.737; most accessible tissue: Minghui63 young leaf, score: 82.368 |
| vg0605309585 (J) | chr06 | 5309585 | ATG | A | 98.10% | 0.00% | ATG -> A | NA |
LOC_Os06g10320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.278; most accessible tissue: Minghui63 young leaf, score: 82.087 |
| vg0605309600 (J) | chr06 | 5309600 | A | T | 98.00% | 0.00% | A -> T | NA |
LOC_Os06g10320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.162; most accessible tissue: Minghui63 young leaf, score: 83.419 |
| vg0605309659 (J) | chr06 | 5309659 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.629; most accessible tissue: Minghui63 flower, score: 76.374 |
| vg0605309759 (J) | chr06 | 5309759 | CT | CTT | 87.60% | 0.00% | CT -> CTT,C,CTTT | NA |
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10320.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10330.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10320.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10330.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.507; most accessible tissue: Callus, score: 82.241 |
| vg0605309762 (J) | chr06 | 5309762 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.507; most accessible tissue: Callus, score: 82.241 |
| vg0605309966 (J) | chr06 | 5309966 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os06g10320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g10330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10340.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.767; most accessible tissue: Callus, score: 85.554 |
| vg0605310169 (J) | chr06 | 5310169 | A | AT | 86.60% | 0.00% | A -> AT | NA |
LOC_Os06g10320.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10330.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.826; most accessible tissue: Callus, score: 65.669 |
| vg0605310329 (J) | chr06 | 5310329 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os06g10350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.862; most accessible tissue: Callus, score: 68.272 |
| vg0605310539 (J) | chr06 | 5310539 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os06g10340.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os06g10350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g10320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 62.128; most accessible tissue: Callus, score: 88.672 |
| vg0605310590 (J) | chr06 | 5310590 | G | T | 97.90% | 0.00% | G -> T | NA |
LOC_Os06g10340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 65.955; most accessible tissue: Minghui63 flower, score: 77.844 |