24 variations found. LOC_Os03g08280 (peptidase; T1 family; putative; expressed), ranging from 4,210,492 bp to 4,213,005 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0304210499 (J) | chr03 | 4210499 | A | G | 98.10% | 0.00% | A -> G | NA |
LOC_Os03g08280.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.576; most accessible tissue: Minghui63 flag leaf, score: 94.503 |
| vg0304210573 (J) | chr03 | 4210573 | T | TA | 99.90% | 0.00% | T -> TA | NA |
LOC_Os03g08280.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g08280.2 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g08280.3 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g08270.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: TA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: TA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.864; most accessible tissue: Minghui63 flag leaf, score: 95.295 |
| vg0304210594 (J) | chr03 | 4210594 | A | C | 97.80% | 0.00% | A -> C | NA |
LOC_Os03g08280.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.830; most accessible tissue: Minghui63 flag leaf, score: 95.545 |
| vg0304210704 (J) | chr03 | 4210704 | A | G | 97.70% | 0.00% | A -> G | NA |
LOC_Os03g08280.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.711; most accessible tissue: Minghui63 flag leaf, score: 94.329 |
| vg0304211266 (J) | chr03 | 4211266 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os03g08270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g08270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08280.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g08280.2 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g08280.3 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.928; most accessible tissue: Minghui63 flag leaf, score: 90.831 |
| vg0304211408 (J) | chr03 | 4211408 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os03g08270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.670; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
| vg0304211437 (J) | chr03 | 4211437 | G | T | 84.70% | 0.00% | G -> T |
mr1002 (Jap_All); LR P-value: 5.54E-07;
mr1011 (Jap_All); LMM P-value: 5.30E-06; LR P-value: 5.30E-06; mr1013 (Jap_All); LR P-value: 2.59E-08; mr1031 (Jap_All); LR P-value: 1.66E-08; mr1034 (Jap_All); LR P-value: 1.54E-07; mr1056 (Jap_All); LR P-value: 3.68E-07; mr1063 (Jap_All); LR P-value: 2.16E-06; mr1163 (Jap_All); LR P-value: 5.24E-07; mr1252 (Jap_All); LR P-value: 7.90E-07; mr1354 (All); LR P-value: 2.55E-07; mr1449 (All); LR P-value: 1.22E-12; mr1554 (All); LR P-value: 5.14E-08; mr1602 (All); LR P-value: 9.17E-06; mr1668 (All); LR P-value: 2.45E-07; mr1671 (Jap_All); LR P-value: 1.91E-06; mr1870 (Jap_All); LR P-value: 1.89E-07; mr1871 (All); LR P-value: 1.29E-13; mr1880 (All); LR P-value: 2.32E-06; mr1905 (All); LR P-value: 1.07E-09; mr1002_2 (Jap_All); LR P-value: 1.14E-08; mr1011_2 (Jap_All); LR P-value: 2.33E-06; mr1013_2 (Jap_All); LR P-value: 3.01E-09; mr1031_2 (Jap_All); LR P-value: 9.78E-11; mr1042_2 (All); LR P-value: 5.64E-21; mr1072_2 (Jap_All); LR P-value: 1.26E-06; mr1075_2 (Jap_All); LR P-value: 6.11E-06; mr1077_2 (Jap_All); LR P-value: 4.41E-06; mr1097_2 (All); LR P-value: 7.92E-13; mr1129_2 (Jap_All); LR P-value: 2.74E-06; mr1180_2 (Jap_All); LR P-value: 2.72E-07; mr1183_2 (Jap_All); LR P-value: 2.19E-07; mr1295_2 (All); LR P-value: 9.84E-06; mr1350_2 (Jap_All); LR P-value: 2.37E-07; mr1354_2 (All); LR P-value: 8.05E-10; mr1361_2 (Jap_All); LR P-value: 3.97E-09; mr1388_2 (All); LR P-value: 4.41E-09; mr1449_2 (All); LR P-value: 4.93E-09; mr1502_2 (All); LR P-value: 1.96E-08; mr1543_2 (All); LR P-value: 2.11E-10; mr1554_2 (All); LR P-value: 3.40E-08; mr1671_2 (Jap_All); LR P-value: 1.44E-09; mr1680_2 (All); LR P-value: 4.10E-13; mr1742_2 (All); LR P-value: 1.19E-15; mr1794_2 (Jap_All); LR P-value: 6.13E-08; mr1805_2 (Jap_All); LR P-value: 6.47E-08; mr1851_2 (All); LR P-value: 6.72E-09; mr1870_2 (Jap_All); LR P-value: 5.99E-07; mr1871_2 (All); LR P-value: 5.37E-24; mr1902_2 (Jap_All); LR P-value: 7.47E-06; mr1966_2 (All); LR P-value: 5.69E-09; mr1966_2 (Jap_All); LR P-value: 1.01E-06 |
LOC_Os03g08270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.210; most accessible tissue: Callus, score: 89.101 |
| vg0304211488 (J) | chr03 | 4211488 | TTGA | T | 97.80% | 0.00% | TTGA -> T | NA |
LOC_Os03g08270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.958; most accessible tissue: Callus, score: 89.101 |
| vg0304211853 (J) | chr03 | 4211853 | G | C | 84.80% | 0.00% | G -> C |
mr1002 (Jap_All); LR P-value: 4.72E-06;
mr1006 (Jap_All); LR P-value: 3.42E-06; mr1011 (Jap_All); LMM P-value: 3.27E-06; LR P-value: 3.27E-06; mr1013 (Jap_All); LR P-value: 7.31E-09; mr1031 (Jap_All); LR P-value: 7.04E-09; mr1034 (Jap_All); LR P-value: 5.96E-08; mr1052 (Jap_All); LR P-value: 5.09E-06; mr1056 (Jap_All); LR P-value: 1.48E-07; mr1063 (Jap_All); LR P-value: 9.34E-07; mr1163 (Jap_All); LR P-value: 2.46E-07; mr1183 (Jap_All); LR P-value: 2.14E-06; mr1252 (Jap_All); LR P-value: 1.87E-07; mr1354 (All); LR P-value: 2.24E-07; mr1449 (All); LR P-value: 3.09E-13; mr1503 (Jap_All); LR P-value: 7.74E-06; mr1554 (All); LR P-value: 6.66E-08; mr1668 (All); LR P-value: 8.72E-08; mr1671 (Jap_All); LR P-value: 7.42E-07; mr1870 (Jap_All); LR P-value: 5.54E-08; mr1871 (All); LR P-value: 8.19E-14; mr1880 (All); LR P-value: 1.90E-06; mr1002_2 (Jap_All); LR P-value: 1.09E-07; mr1011_2 (Jap_All); LR P-value: 3.26E-06; mr1013_2 (Jap_All); LR P-value: 2.99E-09; mr1031_2 (Jap_All); LR P-value: 1.23E-10; mr1042_2 (All); LR P-value: 3.82E-21; mr1072_2 (Jap_All); LR P-value: 8.08E-07; mr1075_2 (Jap_All); LR P-value: 3.38E-06; mr1077_2 (Jap_All); LR P-value: 3.51E-06; mr1097_2 (All); LR P-value: 1.60E-13; mr1115_2 (Jap_All); LR P-value: 1.18E-14; mr1129_2 (Jap_All); LR P-value: 2.24E-06; mr1180_2 (Jap_All); LR P-value: 2.28E-07; mr1183_2 (Jap_All); LR P-value: 1.36E-07; mr1295_2 (All); LR P-value: 6.37E-06; mr1295_2 (Jap_All); LR P-value: 8.30E-06; mr1350_2 (Jap_All); LR P-value: 2.92E-07; mr1354_2 (All); LR P-value: 6.61E-10; mr1388_2 (All); LR P-value: 6.02E-09; mr1479_2 (All); LR P-value: 1.94E-06; mr1502_2 (All); LR P-value: 1.19E-08; mr1543_2 (All); LR P-value: 3.09E-10; mr1554_2 (All); LR P-value: 4.40E-08; mr1671_2 (Jap_All); LR P-value: 1.59E-09; mr1680_2 (All); LR P-value: 2.46E-13; mr1742_2 (All); LR P-value: 2.62E-15; mr1794_2 (Jap_All); LR P-value: 3.31E-08; mr1805_2 (Jap_All); LR P-value: 4.21E-08; mr1851_2 (All); LR P-value: 5.83E-09; mr1870_2 (Jap_All); LR P-value: 1.64E-07; mr1871_2 (All); LR P-value: 8.23E-24; mr1902_2 (Jap_All); LR P-value: 5.42E-06; mr1952_2 (Jap_All); LR P-value: 4.35E-08; mr1966_2 (All); LR P-value: 3.77E-09; mr1966_2 (Jap_All); LR P-value: 6.30E-07 |
LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08284.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.144; most accessible tissue: Minghui63 flower, score: 65.096 |
| vg0304211945 (J) | chr03 | 4211945 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os03g08270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08284.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.225; most accessible tissue: Callus, score: 84.538 |
| vg0304212264 (J) | chr03 | 4212264 | GAC | G | 99.70% | 0.00% | GAC -> G | NA |
LOC_Os03g08270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g08284.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08280.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g08280.2 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g08280.3 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.122; most accessible tissue: Callus, score: 91.123 |
| vg0304212268 (J) | chr03 | 4212268 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os03g08270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08284.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.619; most accessible tissue: Callus, score: 91.123 |
| vg0304212270 (J) | chr03 | 4212270 | CACA | C | 97.20% | 0.28% | CACA -> C,TACA,CAA CA | NA |
LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08284.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: CAACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: CAACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: CAACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: CAACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: TACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: TACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: TACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: TACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.675; most accessible tissue: Callus, score: 91.123 |
| vg0304212272 (J) | chr03 | 4212272 | CA | CAA | 68.50% | 0.00% | CA -> CAA,C,CAAA ,CAAAA | NA |
LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08284.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.1 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.2 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.671; most accessible tissue: Callus, score: 91.123 |
| vg0304212428 (J) | chr03 | 4212428 | A | C | 97.70% | 0.00% | A -> C | NA |
LOC_Os03g08280.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g08280.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g08280.3 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 78.386; most accessible tissue: Callus, score: 90.302 |
| vg0304212487 (J) | chr03 | 4212487 | A | G | 58.50% | 0.00% | G -> A |
LOC_Os03g08280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.316; most accessible tissue: Callus, score: 90.302 |
|
| vg0304212542 (J) | chr03 | 4212542 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os03g08280.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g08270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08280.2 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os03g08280.3 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.190; most accessible tissue: Zhenshan97 flower, score: 91.386 |
| vg0304212850 (J) | chr03 | 4212850 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os03g08280.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g08280.2 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g08280.3 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g08270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.065; most accessible tissue: Zhenshan97 flower, score: 97.767 |
| vg0304212879 (J) | chr03 | 4212879 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g08280.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g08280.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g08280.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g08270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.392; most accessible tissue: Zhenshan97 flower, score: 98.012 |
| vg0304212897 (J) | chr03 | 4212897 | CGGGTGG G | C | 84.80% | 0.00% | CGGGTGGG -> C | NA |
LOC_Os03g08280.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.660; most accessible tissue: Zhenshan97 flower, score: 98.173 |
| vg0304212906 (J) | chr03 | 4212906 | T | C | 84.80% | 0.00% | T -> C | NA |
LOC_Os03g08280.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.757; most accessible tissue: Zhenshan97 flower, score: 98.247 |
| vg0304212973 (J) | chr03 | 4212973 | A | G | 97.80% | 0.00% | A -> G | NA |
LOC_Os03g08280.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08280.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08280.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08270.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g08284.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.145; most accessible tissue: Callus, score: 99.151 |
| vg0304212996 (J) | chr03 | 4212996 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g08280.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g08280.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g08280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08270.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g08284.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.098; most accessible tissue: Callus, score: 99.151 |
| STR0304212889 (J) | chr03 | 4212889 | CGCCGCC GC | CG | 89.00% | 0.00% | CGCCGCCGC -> CG | NA |
|