22 variations found. LOC_Os04g19010 (retrotransposon protein; putative; unclassified), ranging from 10,565,034 bp to 10,565,322 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565042 (J) | chr04 | 10565042 | G | T | 38.50% | 60.03% | G -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 9.241; most accessible tissue: Callus, score: 40.117 |
| vg0410565061 (J) | chr04 | 10565061 | C | T | 24.30% | 60.37% | C -> T |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1121 (Jap_All); LR P-value: 3.42E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1206 (Jap_All); LR P-value: 4.91E-07; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1449 (Jap_All); LR P-value: 3.88E-08; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1844 (Jap_All); LR P-value: 6.15E-06; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.325; most accessible tissue: Callus, score: 40.117 |
| vg0410565071 (J) | chr04 | 10565071 | G | A | 24.40% | 60.26% | G -> A |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1121 (Jap_All); LR P-value: 3.42E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1206 (Jap_All); LR P-value: 4.91E-07; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1449 (Jap_All); LR P-value: 3.88E-08; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1844 (Jap_All); LR P-value: 6.15E-06; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.325; most accessible tissue: Callus, score: 40.117 |
| vg0410565076 (J) | chr04 | 10565076 | G | C | 39.50% | 59.84% | G -> C | NA |
LOC_Os04g19010.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.075; most accessible tissue: Callus, score: 15.368 |
| vg0410565091 (J) | chr04 | 10565091 | G | A | 39.50% | 56.94% | G -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565096 (J) | chr04 | 10565096 | A | C | 23.80% | 52.26% | A -> C | NA |
LOC_Os04g19010.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565119 (J) | chr04 | 10565119 | A | G | 39.60% | 56.45% | A -> G | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565130 (J) | chr04 | 10565130 | G | A | 39.50% | 56.41% | G -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565136 (J) | chr04 | 10565136 | C | T | 39.40% | 59.90% | C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565141 (J) | chr04 | 10565141 | A | G | 21.40% | 60.54% | A -> G |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1121 (Jap_All); LR P-value: 3.42E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (Jap_All); LR P-value: 4.91E-07; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1449 (Jap_All); LR P-value: 3.88E-08; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1844 (Jap_All); LR P-value: 6.15E-06; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1593_2 (All); LR P-value: 9.37E-12 |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.615; most accessible tissue: Callus, score: 15.368 |
| vg0410565185 (J) | chr04 | 10565185 | C | T | 39.70% | 59.18% | C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.934; most accessible tissue: Callus, score: 40.877 |
| vg0410565194 (J) | chr04 | 10565194 | C | T | 39.90% | 59.23% | C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.934; most accessible tissue: Callus, score: 40.877 |
| vg0410565217 (J) | chr04 | 10565217 | CAT | C | 29.80% | 63.92% | CAT -> C | NA |
LOC_Os04g19010.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565219 (J) | chr04 | 10565219 | TACTCCC GGTC | T | 28.60% | 58.87% | TACTCCCGGT C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565223 (J) | chr04 | 10565223 | C | T | 40.40% | 58.89% | C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.770; most accessible tissue: Callus, score: 40.877 |
| vg0410565233 (J) | chr04 | 10565233 | C | T | 37.70% | 60.16% | C -> T | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565246 (J) | chr04 | 10565246 | G | A | 40.40% | 58.74% | G -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565265 (J) | chr04 | 10565265 | C | G | 40.10% | 59.18% | C -> G | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565271 (J) | chr04 | 10565271 | G | A | 39.80% | 59.27% | G -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565281 (J) | chr04 | 10565281 | G | A | 39.80% | 59.10% | G -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565300 (J) | chr04 | 10565300 | C | G | 39.70% | 59.44% | C -> G | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |
| vg0410565308 (J) | chr04 | 10565308 | T | A | 39.70% | 59.48% | T -> A | NA |
LOC_Os04g19010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g19010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.854; most accessible tissue: Callus, score: 40.877 |