39 variations found. Os05g0110900/LOC_Os05g02020 (protein kinase APK1A; chloroplast precursor; putative; expressed), ranging from 577,143 bp to 580,488 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g02020 | protein kinase APK1A, chloroplast precursor, putative, expressed; RAP ID: Os05g0110900; MSU ID: LOC_Os05g02020 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0500577166 (J) | chr05 | 577166 | TG | T | 96.60% | 0.00% | TG -> T | NA |
LOC_Os05g02020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500577187 (J) | chr05 | 577187 | C | A | 81.30% | 0.00% | A -> C | NA |
LOC_Os05g02020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500577513 (J) | chr05 | 577513 | G | A | 88.80% | 0.00% | G -> A |
LOC_Os05g02020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g02020.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500578074 (J) | chr05 | 578074 | C | T | 81.20% | 0.00% | T -> C | NA |
LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500578306 (J) | chr05 | 578306 | G | A | 69.80% | 0.00% | G -> A |
LOC_Os05g02020.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g02020.2 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500578352 (J) | chr05 | 578352 | T | G | 99.70% | 0.00% | T -> G | NA |
LOC_Os05g02020.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g02020.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500578517 (J) | chr05 | 578517 | T | C | 80.60% | 0.00% | T -> C |
LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500578732 (J) | chr05 | 578732 | A | G | 80.50% | 0.42% | A -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500578975 (J) | chr05 | 578975 | C | T | 81.30% | 0.00% | T -> C | NA |
LOC_Os05g02020.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g02020.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579017 (J) | chr05 | 579017 | C | T | 80.40% | 0.00% | C -> T |
mr1006 (All); LR P-value: 1.89E-06;
mr1013 (Ind_All); LR P-value: 1.54E-06; mr1014 (Ind_All); LR P-value: 4.89E-06; mr1015 (Ind_All); LR P-value: 3.83E-08; mr1031 (Ind_All); LR P-value: 5.67E-07; mr1034 (Ind_All); LR P-value: 6.06E-06; mr1042 (Ind_All); LR P-value: 3.71E-06; mr1052 (All); LR P-value: 1.17E-06; mr1056 (Ind_All); LR P-value: 5.66E-06; mr1291 (Ind_All); LR P-value: 3.04E-06; mr1502 (Ind_All); LR P-value: 1.48E-06; mr1662 (All); LR P-value: 1.04E-06; mr1675 (Ind_All); LR P-value: 1.34E-08; mr1950 (Ind_All); LR P-value: 2.07E-06; mr1030_2 (All); LR P-value: 1.08E-07; mr1274_2 (Ind_All); LR P-value: 6.38E-07; mr1352_2 (Ind_All); LR P-value: 1.15E-12; mr1743_2 (All); LR P-value: 1.79E-06 |
LOC_Os05g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g02020.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579066 (J) | chr05 | 579066 | T | A | 98.90% | 0.00% | T -> A |
LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500579239 (J) | chr05 | 579239 | T | G | 98.80% | 0.00% | T -> G | NA |
LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579268 (J) | chr05 | 579268 | T | C | 99.30% | 0.00% | T -> C | NA |
LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579278 (J) | chr05 | 579278 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579291 (J) | chr05 | 579291 | C | T | 75.60% | 0.00% | C -> T |
LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500579418 (J) | chr05 | 579418 | A | C | 98.90% | 0.00% | A -> C | NA |
LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579546 (J) | chr05 | 579546 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579647 (J) | chr05 | 579647 | GA | G | 73.00% | 3.00% | GA -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579649 (J) | chr05 | 579649 | AATT | AT | 70.70% | 14.73% | AATT -> A,AT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579650 (J) | chr05 | 579650 | ATTT | ATT | 59.40% | 22.05% | ATTT -> ATT,AT,A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579651 (J) | chr05 | 579651 | T | A | 59.10% | 28.31% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579652 (J) | chr05 | 579652 | T | A | 42.50% | 39.46% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579657 (J) | chr05 | 579657 | TA | TTAA | 62.20% | 1.63% | TTAA -> TA,T,TATAA ,ATAA | NA |
LOC_Os05g02010.1 Alt: TATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: TATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TATAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TATAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: ATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: ATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: ATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: ATAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: ATAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: ATAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579658 (J) | chr05 | 579658 | TAA | AAA | 51.30% | 27.55% | TAA -> TA,AAA,TAA AAA,TAAAAA A,TAAAA,T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: TAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: TAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: TAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: TAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: TAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: TAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: TAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: TAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: TAAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: TAAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: AAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: AAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579659 (J) | chr05 | 579659 | A | T | 97.70% | 0.00% | A -> T | NA |
LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579675 (J) | chr05 | 579675 | GA | G | 67.30% | 0.00% | G -> GA,GAA | NA |
LOC_Os05g02010.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579714 (J) | chr05 | 579714 | CTAAGAA CACAAGT TGATAGT G | C | 80.40% | 0.00% | C -> CTAAGAACAC AAGTTGATAG TG,CTAAGAA CACAAGTTGA TTGTG | NA |
LOC_Os05g02010.1 Alt: CTAAGAACACAAGTTGATAGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.2 Alt: CTAAGAACACAAGTTGATAGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: CTAAGAACACAAGTTGATAGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: CTAAGAACACAAGTTGATAGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: CTAAGAACACAAGTTGATAGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: CTAAGAACACAAGTTGATAGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: CTAAGAACACAAGTTGATTGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: CTAAGAACACAAGTTGATTGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: CTAAGAACACAAGTTGATTGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: CTAAGAACACAAGTTGATTGTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: CTAAGAACACAAGTTGATTGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: CTAAGAACACAAGTTGATTGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579931 (J) | chr05 | 579931 | G | A | 80.80% | 0.00% | A -> G | NA |
LOC_Os05g02020.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500579946 (J) | chr05 | 579946 | G | A | 81.50% | 0.08% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02020.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580001 (J) | chr05 | 580001 | C | A | 76.60% | 0.11% | C -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02020.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580213 (J) | chr05 | 580213 | T | C | 74.90% | 0.13% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g02020.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580227 (J) | chr05 | 580227 | G | A | 95.20% | 0.00% | G -> A |
LOC_Os05g02020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580321 (J) | chr05 | 580321 | C | A | 95.20% | 0.00% | C -> A |
LOC_Os05g02020.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580370 (J) | chr05 | 580370 | C | A | 89.20% | 0.00% | C -> A |
LOC_Os05g02020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0500580401 (J) | chr05 | 580401 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os05g02020.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500580428 (J) | chr05 | 580428 | AGAG | A | 99.10% | 0.00% | AGAG -> A | NA |
LOC_Os05g02020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500580447 (J) | chr05 | 580447 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os05g02020.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g02020.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g02010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g02010.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g02010.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g02010.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500580483 (J) | chr05 | 580483 | G | T | 97.70% | 0.00% | G -> T |
LOC_Os05g02020.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g02020.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g02010.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| STR0500577185 (J) | chr05 | 577185 | AAC | AAA | 68.60% | 0.00% | AAA -> AAC | NA |
|