253 variations found. Os04g0111900/LOC_Os04g02110 (disease resistance protein RGA3; putative; expressed), ranging from 681,114 bp to 687,716 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g02110 | disease resistance protein RGA3, putative, expressed; RAP ID: Os04g0111900; MSU ID: LOC_Os04g02110 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os04g02110 | Os04g0111900 | an NBS-LRR class R-gene. EF642270-EF642284 (O. sativa, O. rufipogon, O. nivara). FJ709783-FJ709799 (O. sativa, O. rufipogon, O. glumipatula). | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0400682192 (J) | chr04 | 682192 | AA | A | 87.00% | 0.00% | AA -> A | NA |
|
| vg0400681122 (J) | chr04 | 681122 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.254; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0400681124 (J) | chr04 | 681124 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.244; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0400681125 (J) | chr04 | 681125 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os04g02110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.275; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0400681129 (J) | chr04 | 681129 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.712; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0400681136 (J) | chr04 | 681136 | C | T | 88.80% | 8.57% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.360; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0400681144 (J) | chr04 | 681144 | G | A | 89.20% | 8.38% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.382; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0400681146 (J) | chr04 | 681146 | C | T | 89.00% | 8.25% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.456; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0400681147 (J) | chr04 | 681147 | G | A | 97.00% | 0.95% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.592; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0400681151 (J) | chr04 | 681151 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.664; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0400681156 (J) | chr04 | 681156 | T | C | 98.40% | 0.00% | T -> C | NA |
LOC_Os04g02110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.245; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0400681157 (J) | chr04 | 681157 | G | A | 95.50% | 2.62% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.238; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0400681160 (J) | chr04 | 681160 | G | A | 96.00% | 2.12% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.939; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0400681161 (J) | chr04 | 681161 | T | A | 90.40% | 0.78% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.942; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0400681164 (J) | chr04 | 681164 | T | C | 62.30% | 2.14% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.167; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0400681165 (J) | chr04 | 681165 | G | A | 97.90% | 1.04% | G -> A,GACAACAG GA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: GACAACAGGA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: GACAACAGGA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: GACAACAGGA| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: GACAACAGGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: GACAACAGGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.167; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0400681169 (J) | chr04 | 681169 | A | ACAGTGG TT | 98.30% | 0.91% | A -> ACAG,ACAGT GGT,ACAGTG GTT,ACAGTG G | NA |
LOC_Os04g02110.1 Alt: ACAGTGGTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: ACAGTGGTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: ACAGTGGTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: ACAGTGGTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: ACAGTGGTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: ACAGTGGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: ACAGTGGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: ACAGTGGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: ACAGTGGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: ACAGTGGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: ACAG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: ACAG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: ACAG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: ACAG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: ACAG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.1 Alt: ACAGTGG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: ACAGTGG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: ACAGTGG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: ACAGTGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: ACAGTGG| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159 |
| vg0400681170 (J) | chr04 | 681170 | C | T | 79.30% | 2.07% | T -> C,TTGGCGCC G |
mr1013 (Jap_All); LR P-value: 2.71E-06;
mr1031 (All); LR P-value: 1.18E-12; mr1031 (Jap_All); LR P-value: 2.89E-07; mr1056 (All); LR P-value: 6.38E-13; mr1056 (Jap_All); LR P-value: 7.55E-07; mr1252 (All); LR P-value: 9.52E-07; mr1549 (Jap_All); LR P-value: 1.61E-08; mr1555 (All); LR P-value: 5.01E-06; mr1668 (Jap_All); LR P-value: 7.99E-07; mr1757 (Jap_All); LR P-value: 7.76E-09; mr1829 (Jap_All); LR P-value: 6.52E-06; mr1871 (Jap_All); LR P-value: 2.02E-06; mr1011_2 (All); LR P-value: 2.09E-09; mr1011_2 (Jap_All); LR P-value: 3.38E-06; mr1013_2 (All); LR P-value: 3.29E-16; mr1013_2 (Jap_All); LR P-value: 2.80E-08; mr1031_2 (Jap_All); LR P-value: 4.10E-08; mr1042_2 (Jap_All); LR P-value: 3.27E-08; mr1045_2 (All); LR P-value: 1.21E-07; mr1045_2 (Jap_All); LR P-value: 4.40E-06; mr1063_2 (Jap_All); LR P-value: 4.41E-07; mr1077_2 (Jap_All); LR P-value: 2.44E-06; mr1115_2 (All); LR P-value: 1.08E-24; mr1121_2 (Jap_All); LR P-value: 1.22E-06; mr1161_2 (Jap_All); LR P-value: 4.34E-07; mr1174_2 (All); LMM P-value: 8.12E-06; mr1206_2 (Jap_All); LR P-value: 1.96E-07; mr1229_2 (All); LR P-value: 8.39E-09; mr1229_2 (Jap_All); LR P-value: 3.22E-09; mr1236_2 (Jap_All); LR P-value: 1.30E-06; mr1248_2 (All); LR P-value: 6.23E-14; mr1250_2 (All); LR P-value: 4.17E-07; mr1251_2 (All); LR P-value: 2.17E-36; mr1251_2 (Jap_All); LR P-value: 4.83E-09; mr1252_2 (All); LMM P-value: 1.94E-07; LR P-value: 5.16E-11; mr1252_2 (Jap_All); LR P-value: 2.92E-08; mr1263_2 (All); LR P-value: 7.31E-07; mr1263_2 (Jap_All); LR P-value: 1.80E-08; mr1423_2 (Jap_All); LR P-value: 1.06E-06; mr1435_2 (Jap_All); LR P-value: 5.00E-09; mr1441_2 (Jap_All); LR P-value: 5.37E-06; mr1482_2 (All); LR P-value: 2.31E-07; mr1502_2 (Jap_All); LR P-value: 4.44E-09; mr1543_2 (Jap_All); LR P-value: 5.46E-10; mr1544_2 (Jap_All); LR P-value: 3.24E-06; mr1550_2 (Jap_All); LR P-value: 6.64E-07; mr1555_2 (All); LR P-value: 1.07E-07; mr1563_2 (Jap_All); LR P-value: 1.36E-07; mr1580_2 (Jap_All); LR P-value: 7.51E-11; mr1596_2 (All); LR P-value: 8.57E-06; mr1596_2 (Jap_All); LR P-value: 2.34E-06; mr1599_2 (Jap_All); LR P-value: 2.21E-08; mr1611_2 (All); LR P-value: 8.84E-24; mr1617_2 (All); LR P-value: 4.43E-26; mr1680_2 (All); LMM P-value: 2.28E-06; mr1680_2 (Jap_All); LR P-value: 6.00E-08; mr1693_2 (All); LR P-value: 5.69E-07; mr1739_2 (Jap_All); LR P-value: 5.39E-07; mr1741_2 (All); LR P-value: 9.42E-10; mr1741_2 (Jap_All); LR P-value: 6.34E-06; mr1742_2 (Jap_All); LR P-value: 7.74E-09; mr1746_2 (Jap_All); LR P-value: 9.92E-09; mr1757_2 (Jap_All); LR P-value: 5.64E-07; mr1763_2 (All); LR P-value: 1.29E-07; mr1771_2 (All); LR P-value: 6.29E-41; mr1771_2 (Jap_All); LR P-value: 7.19E-11; mr1780_2 (Jap_All); LR P-value: 4.54E-08; mr1784_2 (All); LR P-value: 2.44E-43; mr1784_2 (Jap_All); LR P-value: 1.25E-10; mr1785_2 (All); LR P-value: 8.23E-08; mr1789_2 (All); LR P-value: 2.11E-28; mr1800_2 (All); LR P-value: 9.09E-15; mr1825_2 (Jap_All); LR P-value: 9.30E-10; mr1829_2 (Jap_All); LR P-value: 2.91E-06; mr1837_2 (All); LR P-value: 8.09E-08; mr1844_2 (All); LR P-value: 1.30E-13; mr1844_2 (Jap_All); LR P-value: 1.90E-06; mr1862_2 (Jap_All); LR P-value: 2.94E-09; mr1871_2 (All); LMM P-value: 2.10E-06; mr1871_2 (Jap_All); LR P-value: 6.84E-10; mr1880_2 (All); LMM P-value: 6.07E-06; LR P-value: 2.72E-09; mr1880_2 (Jap_All); LR P-value: 2.07E-09; mr1887_2 (All); LMM P-value: 3.68E-06; mr1887_2 (Jap_All); LR P-value: 9.25E-07; mr1902_2 (Jap_All); LR P-value: 1.59E-07; mr1952_2 (Jap_All); LR P-value: 8.60E-09 |
LOC_Os04g02110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: TTGGCGCCG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: TTGGCGCCG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: TTGGCGCCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: TTGGCGCCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: TTGGCGCCG| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.299; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0400681171 (J) | chr04 | 681171 | A | AGTTGGC GC | 98.30% | 1.40% | A -> AGTTGG,AGT TGGCGC,ACT T,AGTTGGCG CCGAC,ACTT CTTAAAACTT G | NA |
LOC_Os04g02110.1 Alt: AGTTGGCGC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: AGTTGGCGC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: AGTTGGCGC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: AGTTGGCGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: AGTTGGCGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: ACTT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: ACTT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: ACTT| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: ACTT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: ACTT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.1 Alt: AGTTGG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: AGTTGG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: AGTTGG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: AGTTGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: AGTTGG| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: ACTTCTTAAAACTTG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: ACTTCTTAAAACTTG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: ACTTCTTAAAACTTG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: ACTTCTTAAAACTTG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: ACTTCTTAAAACTTG| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.1 Alt: AGTTGGCGCCGAC| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02110.3 Alt: AGTTGGCGCCGAC| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os04g02090.1 Alt: AGTTGGCGCCGAC| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g02100.1 Alt: AGTTGGCGCCGAC| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g02110.2 Alt: AGTTGGCGCCGAC| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.336; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0400681172 (J) | chr04 | 681172 | C | G | 96.00% | 1.27% | C -> G,CT | NA |
LOC_Os04g02110.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.321; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0400681174 (J) | chr04 | 681174 | A | C | 98.30% | 1.42% | A -> T,C | NA |
LOC_Os04g02110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.174; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0400681177 (J) | chr04 | 681177 | AT | A | 98.30% | 1.31% | AT -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 |
| vg0400681180 (J) | chr04 | 681180 | C | A | 67.10% | 2.01% | A -> C,T | NA |
LOC_Os04g02110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g02110.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.314; most accessible tissue: Minghui63 flag leaf, score: 87.052 |
| vg0400681200 (J) | chr04 | 681200 | TCCTAAA AAACAC | T | 96.10% | 2.31% | TCCTAAAAAA CAC -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 |
| vg0400681203 (J) | chr04 | 681203 | T | TA | 95.60% | 1.04% | T -> TA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g02110.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.3 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02090.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02100.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g02110.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 |
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