24 variations found. LOC_Os08g07920 (disease resistance protein RPM1; putative; expressed), ranging from 4,462,148 bp to 4,464,256 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0804462336 (J) | chr08 | 4462336 | AC | ACC | 33.20% | 63.14% | AC -> ACC,ACCC,A | NA |
LOC_Os08g07920.1 Alt: ACCC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g07920.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g07920.1 Alt: ACC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g07920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.029; most accessible tissue: Callus, score: 47.148 |
| vg0804462446 (J) | chr08 | 4462446 | G | A | 34.60% | 64.16% | G -> A | NA |
LOC_Os08g07920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g07920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.166; most accessible tissue: Callus, score: 76.262 |
| vg0804462517 (J) | chr08 | 4462517 | C | T | 33.90% | 63.52% | C -> T | NA |
LOC_Os08g07920.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g07920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.914; most accessible tissue: Callus, score: 76.262 |
| vg0804462937 (J) | chr08 | 4462937 | GAGGCAA CT | G | 34.80% | 63.63% | GAGGCAACT -> G | NA |
LOC_Os08g07920.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g07920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.183; most accessible tissue: Callus, score: 80.370 |
| vg0804463121 (J) | chr08 | 4463121 | GT | G | 24.10% | 65.83% | GT -> GTT,G | NA |
LOC_Os08g07900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.178; most accessible tissue: Callus, score: 47.315 |
| vg0804463130 (J) | chr08 | 4463130 | TA | T | 33.40% | 65.38% | TA -> T,AA,TAA | NA |
LOC_Os08g07900.1 Alt: AA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: AA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: AA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: AA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.026; most accessible tissue: Callus, score: 47.315 |
| vg0804463131 (J) | chr08 | 4463131 | A | T | 31.80% | 64.35% | A -> T | NA |
LOC_Os08g07900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.026; most accessible tissue: Callus, score: 47.315 |
| vg0804463132 (J) | chr08 | 4463132 | A | T | 34.40% | 64.18% | A -> T | NA |
LOC_Os08g07900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.026; most accessible tissue: Callus, score: 47.315 |
| vg0804463333 (J) | chr08 | 4463333 | G | GT | 34.30% | 64.85% | G -> GT | NA |
LOC_Os08g07900.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 9.750; most accessible tissue: Callus, score: 44.628 |
| vg0804463684 (J) | chr08 | 4463684 | C | A | 38.80% | 57.00% | C -> A | NA |
LOC_Os08g07900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.549; most accessible tissue: Callus, score: 29.336 |
| vg0804463706 (J) | chr08 | 4463706 | A | C | 34.20% | 64.66% | A -> C | NA |
LOC_Os08g07900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.334; most accessible tissue: Callus, score: 29.336 |
| vg0804463707 (J) | chr08 | 4463707 | A | G | 34.20% | 64.66% | A -> G | NA |
LOC_Os08g07900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.334; most accessible tissue: Callus, score: 29.336 |
| vg0804463714 (J) | chr08 | 4463714 | T | G | 34.30% | 64.64% | T -> G | NA |
LOC_Os08g07900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.719; most accessible tissue: Callus, score: 29.336 |
| vg0804463718 (J) | chr08 | 4463718 | T | A | 34.30% | 64.64% | T -> A | NA |
LOC_Os08g07900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.807; most accessible tissue: Callus, score: 29.336 |
| vg0804463753 (J) | chr08 | 4463753 | C | A | 36.00% | 62.63% | C -> A | NA |
LOC_Os08g07900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 15.069; most accessible tissue: Callus, score: 29.336 |
| vg0804463760 (J) | chr08 | 4463760 | CTTTTCT TTCCTA | C | 36.90% | 62.29% | CTTTTCTTTC CTA -> C | NA |
LOC_Os08g07900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 15.174; most accessible tissue: Callus, score: 29.336 |
| vg0804463773 (J) | chr08 | 4463773 | T | C | 38.30% | 61.09% | T -> C | NA |
LOC_Os08g07900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.940; most accessible tissue: Callus, score: 29.336 |
| vg0804463783 (J) | chr08 | 4463783 | C | T | 38.20% | 61.09% | C -> T |
mr1004 (All); LR P-value: 3.52E-07;
mr1006 (All); LR P-value: 1.82E-07; mr1052 (All); LR P-value: 9.47E-08; mr1158 (All); LR P-value: 1.77E-15; mr1209 (All); LR P-value: 6.05E-06; mr1230 (All); LR P-value: 2.58E-07; mr1321 (All); LR P-value: 1.53E-06; mr1348 (All); LR P-value: 8.78E-09; mr1349 (All); LR P-value: 9.34E-06; mr1365 (All); LR P-value: 2.39E-06; mr1545 (All); LR P-value: 2.51E-06; mr1621 (All); LR P-value: 5.70E-08; mr1665 (All); LR P-value: 4.75E-06; mr1939 (All); LR P-value: 1.75E-09 |
LOC_Os08g07900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.690; most accessible tissue: Callus, score: 29.336 |
| vg0804463806 (J) | chr08 | 4463806 | G | T | 33.70% | 64.68% | G -> T,GT | NA |
LOC_Os08g07900.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.644; most accessible tissue: Callus, score: 29.336 |
| vg0804463813 (J) | chr08 | 4463813 | T | C | 34.80% | 63.65% | T -> C | NA |
LOC_Os08g07900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.800; most accessible tissue: Callus, score: 29.336 |
| vg0804463814 (J) | chr08 | 4463814 | G | A | 34.60% | 63.63% | G -> A | NA |
LOC_Os08g07900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.800; most accessible tissue: Callus, score: 29.336 |
| vg0804463836 (J) | chr08 | 4463836 | T | C | 35.60% | 63.44% | T -> C | NA |
LOC_Os08g07900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 13.931; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0804463972 (J) | chr08 | 4463972 | G | A | 34.20% | 65.13% | G -> A | NA |
LOC_Os08g07900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.876; most accessible tissue: Callus, score: 66.402 |
| vg0804464111 (J) | chr08 | 4464111 | C | CA | 25.10% | 65.81% | C -> CA,CAA,CAA A | NA |
LOC_Os08g07900.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g07910.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g07900.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07910.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07930.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g07920.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 14.629; most accessible tissue: Callus, score: 60.841 |