16 variations found. LOC_Os04g55740 (peroxidase precursor; putative; expressed), ranging from 33,179,631 bp to 33,181,419 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0433179735 (J) | chr04 | 33179735 | A | T | 99.50% | 0.00% | A -> T | NA |
LOC_Os04g55740.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g55730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.793; most accessible tissue: Callus, score: 98.666 |
| vg0433179897 (J) | chr04 | 33179897 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os04g55740.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g55730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.081; most accessible tissue: Minghui63 panicle, score: 92.078 |
| vg0433180017 (J) | chr04 | 33180017 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g55740.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os04g55730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.117; most accessible tissue: Callus, score: 92.968 |
| vg0433180233 (J) | chr04 | 33180233 | G | C | 99.50% | 0.00% | G -> C,T | NA |
LOC_Os04g55740.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g55740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 85.235; most accessible tissue: Minghui63 root, score: 90.044 |
| vg0433180461 (J) | chr04 | 33180461 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os04g55740.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os04g55730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.578; most accessible tissue: Minghui63 root, score: 88.642 |
| vg0433180567 (J) | chr04 | 33180567 | T | G | 57.60% | 0.00% | G -> T |
mr1024_2 (All); LR P-value: 1.45E-24;
mr1084_2 (All); LR P-value: 1.06E-08; mr1151_2 (All); LR P-value: 7.51E-14; mr1198_2 (All); LR P-value: 3.90E-10; mr1205_2 (All); LR P-value: 5.12E-08; mr1217_2 (All); LR P-value: 5.41E-13; mr1227_2 (All); LR P-value: 1.60E-06; mr1228_2 (All); LR P-value: 7.31E-11; mr1275_2 (All); LR P-value: 1.79E-06; mr1298_2 (All); LR P-value: 1.56E-21; mr1302_2 (All); LR P-value: 6.29E-08; mr1405_2 (All); LR P-value: 1.58E-06; mr1418_2 (All); LR P-value: 3.16E-07; mr1488_2 (All); LR P-value: 4.81E-07; mr1506_2 (All); LR P-value: 1.63E-10; mr1521_2 (All); LR P-value: 1.37E-12; mr1604_2 (All); LR P-value: 3.65E-08; mr1646_2 (All); LR P-value: 6.12E-10; mr1681_2 (All); LR P-value: 3.88E-08; mr1698_2 (All); LR P-value: 2.75E-21; mr1728_2 (All); LR P-value: 1.88E-11; mr1731_2 (All); LR P-value: 1.14E-21; mr1751_2 (All); LR P-value: 4.29E-09; mr1824_2 (All); LR P-value: 5.52E-08; mr1834_2 (All); LR P-value: 2.84E-06; mr1869_2 (All); LR P-value: 9.04E-06; mr1885_2 (All); LR P-value: 3.80E-08; mr1924_2 (All); LR P-value: 7.88E-23; mr1940_2 (All); LR P-value: 3.10E-09; mr1950_2 (All); LR P-value: 1.64E-15; mr1992_2 (All); LR P-value: 9.90E-06 |
LOC_Os04g55730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g55740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.671; most accessible tissue: Minghui63 root, score: 89.995 |
| vg0433180589 (J) | chr04 | 33180589 | A | G | 57.10% | 0.00% | G -> A |
mr1024_2 (All); LR P-value: 1.64E-24;
mr1084_2 (All); LR P-value: 6.20E-09; mr1133_2 (All); LR P-value: 2.08E-14; mr1151_2 (All); LR P-value: 5.21E-14; mr1198_2 (All); LR P-value: 6.31E-10; mr1205_2 (All); LR P-value: 3.89E-08; mr1217_2 (All); LR P-value: 5.40E-13; mr1227_2 (All); LR P-value: 1.95E-06; mr1228_2 (All); LR P-value: 4.88E-11; mr1298_2 (All); LR P-value: 1.74E-21; mr1302_2 (All); LR P-value: 7.44E-09; mr1376_2 (All); LR P-value: 2.20E-07; mr1405_2 (All); LR P-value: 1.36E-06; mr1418_2 (All); LR P-value: 6.81E-08; mr1431_2 (All); LR P-value: 8.68E-08; mr1488_2 (All); LR P-value: 1.33E-07; mr1506_2 (All); LR P-value: 3.43E-11; mr1604_2 (All); LR P-value: 8.31E-09; mr1646_2 (All); LR P-value: 6.30E-10; mr1659_2 (All); LR P-value: 7.22E-08; mr1677_2 (All); LR P-value: 9.30E-06; mr1681_2 (All); LR P-value: 3.67E-08; mr1714_2 (All); LR P-value: 1.19E-10; mr1728_2 (All); LR P-value: 8.86E-12; mr1731_2 (All); LR P-value: 1.72E-21; mr1751_2 (All); LR P-value: 1.37E-09; mr1824_2 (All); LR P-value: 7.08E-09; mr1834_2 (All); LR P-value: 2.56E-06; mr1869_2 (All); LR P-value: 6.69E-06; mr1885_2 (All); LR P-value: 2.15E-08; mr1924_2 (All); LR P-value: 4.34E-23; mr1940_2 (All); LR P-value: 5.80E-09; mr1950_2 (All); LR P-value: 8.73E-14; mr1986_2 (All); LR P-value: 4.67E-11; mr1992_2 (All); LR P-value: 3.24E-06 |
LOC_Os04g55740.1 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.756; most accessible tissue: Minghui63 root, score: 90.772 |
| vg0433180655 (J) | chr04 | 33180655 | A | G | 57.60% | 0.02% | G -> A |
mr1913 (All); LR P-value: 3.72E-17;
mr1024_2 (All); LR P-value: 2.64E-24; mr1084_2 (All); LR P-value: 2.37E-08; mr1151_2 (All); LR P-value: 2.87E-13; mr1198_2 (All); LR P-value: 2.80E-09; mr1205_2 (All); LR P-value: 1.46E-07; mr1217_2 (All); LR P-value: 1.24E-12; mr1227_2 (All); LR P-value: 3.23E-06; mr1228_2 (All); LR P-value: 1.03E-10; mr1298_2 (All); LR P-value: 6.24E-22; mr1302_2 (All); LR P-value: 1.45E-07; mr1405_2 (All); LR P-value: 1.61E-06; mr1418_2 (All); LR P-value: 8.12E-07; mr1488_2 (All); LR P-value: 1.09E-06; mr1506_2 (All); LR P-value: 7.40E-10; mr1604_2 (All); LR P-value: 8.99E-08; mr1681_2 (All); LR P-value: 3.89E-08; mr1728_2 (All); LR P-value: 1.03E-11; mr1731_2 (All); LR P-value: 5.08E-22; mr1751_2 (All); LR P-value: 3.02E-09; mr1824_2 (All); LR P-value: 1.53E-07; mr1877_2 (All); LR P-value: 9.46E-22; mr1885_2 (All); LR P-value: 6.08E-08; mr1924_2 (All); LR P-value: 5.35E-23; mr1940_2 (All); LR P-value: 5.42E-09; mr1950_2 (All); LR P-value: 5.48E-14 |
LOC_Os04g55740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g55740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.738; most accessible tissue: Minghui63 root, score: 90.857 |
| vg0433180955 (J) | chr04 | 33180955 | A | AATC | 57.70% | 0.00% | AATC -> A | NA |
LOC_Os04g55730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g55750.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g55740.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.987; most accessible tissue: Callus, score: 91.622 |
| vg0433181052 (J) | chr04 | 33181052 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g55730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g55750.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g55740.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.361; most accessible tissue: Callus, score: 91.622 |
| vg0433181143 (J) | chr04 | 33181143 | A | G | 57.70% | 0.08% | G -> A |
mr1084_2 (All); LR P-value: 3.25E-08;
mr1151_2 (All); LR P-value: 3.22E-13; mr1198_2 (All); LR P-value: 2.77E-09; mr1205_2 (All); LR P-value: 1.17E-07; mr1228_2 (All); LR P-value: 2.17E-10; mr1298_2 (All); LR P-value: 1.22E-21; mr1302_2 (All); LR P-value: 3.61E-08; mr1405_2 (All); LR P-value: 3.15E-06; mr1418_2 (All); LR P-value: 3.28E-07; mr1488_2 (All); LR P-value: 4.73E-07; mr1506_2 (All); LR P-value: 2.05E-10; mr1604_2 (All); LR P-value: 3.47E-08; mr1659_2 (All); LR P-value: 1.16E-07; mr1681_2 (All); LR P-value: 9.35E-08; mr1728_2 (All); LR P-value: 1.34E-11; mr1731_2 (All); LR P-value: 9.30E-22; mr1751_2 (All); LR P-value: 1.32E-09; mr1824_2 (All); LR P-value: 2.82E-08; mr1877_2 (All); LR P-value: 5.10E-22; mr1885_2 (All); LR P-value: 7.64E-08; mr1924_2 (All); LR P-value: 7.09E-23; mr1940_2 (All); LR P-value: 1.98E-08 |
LOC_Os04g55740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g55740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 61.363; most accessible tissue: Minghui63 root, score: 77.565 |
| vg0433181144 (J) | chr04 | 33181144 | A | C | 57.80% | 0.00% | C -> A,G |
mr1084_2 (All); LR P-value: 3.25E-08;
mr1151_2 (All); LR P-value: 3.22E-13; mr1198_2 (All); LR P-value: 2.77E-09; mr1205_2 (All); LR P-value: 1.17E-07; mr1228_2 (All); LR P-value: 2.17E-10; mr1298_2 (All); LR P-value: 1.22E-21; mr1302_2 (All); LR P-value: 3.61E-08; mr1405_2 (All); LR P-value: 3.15E-06; mr1418_2 (All); LR P-value: 3.28E-07; mr1488_2 (All); LR P-value: 4.73E-07; mr1506_2 (All); LR P-value: 2.05E-10; mr1604_2 (All); LR P-value: 3.47E-08; mr1659_2 (All); LR P-value: 1.16E-07; mr1681_2 (All); LR P-value: 9.35E-08; mr1728_2 (All); LR P-value: 1.34E-11; mr1731_2 (All); LR P-value: 9.30E-22; mr1751_2 (All); LR P-value: 1.32E-09; mr1824_2 (All); LR P-value: 2.82E-08; mr1877_2 (All); LR P-value: 5.10E-22; mr1885_2 (All); LR P-value: 7.64E-08; mr1924_2 (All); LR P-value: 7.09E-23; mr1940_2 (All); LR P-value: 1.98E-08 |
LOC_Os04g55740.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os04g55730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g55750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g55740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 61.363; most accessible tissue: Minghui63 root, score: 77.565 |
| vg0433181159 (J) | chr04 | 33181159 | G | A | 57.70% | 0.06% | A -> G |
mr1790 (All); LR P-value: 6.20E-10;
mr1945 (All); LR P-value: 1.39E-09; mr1024_2 (All); LR P-value: 6.93E-25; mr1084_2 (All); LR P-value: 1.95E-08; mr1133_2 (All); LR P-value: 1.83E-14; mr1151_2 (All); LR P-value: 1.00E-13; mr1198_2 (All); LR P-value: 1.93E-09; mr1205_2 (All); LR P-value: 8.32E-08; mr1217_2 (All); LR P-value: 5.52E-13; mr1228_2 (All); LR P-value: 3.69E-11; mr1298_2 (All); LR P-value: 1.36E-22; mr1302_2 (All); LR P-value: 9.74E-08; mr1376_2 (All); LR P-value: 3.05E-07; mr1405_2 (All); LR P-value: 1.36E-06; mr1418_2 (All); LR P-value: 5.76E-07; mr1431_2 (All); LR P-value: 1.16E-07; mr1488_2 (All); LR P-value: 9.02E-07; mr1506_2 (All); LR P-value: 4.26E-10; mr1521_2 (All); LR P-value: 1.22E-12; mr1604_2 (All); LR P-value: 5.50E-08; mr1646_2 (All); LR P-value: 6.78E-10; mr1659_2 (All); LR P-value: 5.18E-08; mr1667_2 (All); LR P-value: 1.14E-10; mr1677_2 (All); LR P-value: 7.36E-06; mr1681_2 (All); LR P-value: 3.55E-08; mr1714_2 (All); LR P-value: 8.00E-11; mr1728_2 (All); LR P-value: 6.14E-12; mr1731_2 (All); LR P-value: 7.51E-23; mr1751_2 (All); LR P-value: 6.45E-10; mr1824_2 (All); LR P-value: 6.60E-08; mr1869_2 (All); LR P-value: 9.01E-06; mr1885_2 (All); LR P-value: 5.31E-08; mr1922_2 (All); LR P-value: 1.73E-19; mr1924_2 (All); LR P-value: 5.92E-24; mr1940_2 (All); LR P-value: 3.76E-09; mr1950_2 (All); LR P-value: 2.96E-14 |
LOC_Os04g55740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g55740.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 62.293; most accessible tissue: Minghui63 root, score: 77.565 |
| vg0433181178 (J) | chr04 | 33181178 | G | T | 57.70% | 0.00% | T -> G |
mr1790 (All); LR P-value: 6.20E-10;
mr1945 (All); LR P-value: 1.39E-09; mr1024_2 (All); LR P-value: 6.93E-25; mr1084_2 (All); LR P-value: 1.95E-08; mr1133_2 (All); LR P-value: 1.83E-14; mr1151_2 (All); LR P-value: 1.00E-13; mr1198_2 (All); LR P-value: 1.93E-09; mr1205_2 (All); LR P-value: 8.32E-08; mr1217_2 (All); LR P-value: 5.52E-13; mr1228_2 (All); LR P-value: 3.69E-11; mr1298_2 (All); LR P-value: 1.36E-22; mr1302_2 (All); LR P-value: 9.74E-08; mr1376_2 (All); LR P-value: 3.05E-07; mr1405_2 (All); LR P-value: 1.36E-06; mr1418_2 (All); LR P-value: 5.76E-07; mr1431_2 (All); LR P-value: 1.16E-07; mr1488_2 (All); LR P-value: 9.02E-07; mr1506_2 (All); LR P-value: 4.26E-10; mr1521_2 (All); LR P-value: 1.22E-12; mr1604_2 (All); LR P-value: 5.50E-08; mr1646_2 (All); LR P-value: 6.78E-10; mr1659_2 (All); LR P-value: 5.18E-08; mr1667_2 (All); LR P-value: 1.14E-10; mr1677_2 (All); LR P-value: 7.36E-06; mr1681_2 (All); LR P-value: 3.55E-08; mr1714_2 (All); LR P-value: 8.00E-11; mr1728_2 (All); LR P-value: 6.14E-12; mr1731_2 (All); LR P-value: 7.51E-23; mr1751_2 (All); LR P-value: 6.45E-10; mr1824_2 (All); LR P-value: 6.60E-08; mr1869_2 (All); LR P-value: 9.01E-06; mr1885_2 (All); LR P-value: 5.31E-08; mr1922_2 (All); LR P-value: 1.73E-19; mr1924_2 (All); LR P-value: 5.92E-24; mr1940_2 (All); LR P-value: 3.76E-09; mr1950_2 (All); LR P-value: 2.96E-14 |
LOC_Os04g55740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 66.176; most accessible tissue: Callus, score: 93.216 |
| vg0433181361 (J) | chr04 | 33181361 | A | ACT | 98.70% | 0.00% | A -> ACT | NA |
LOC_Os04g55740.1 Alt: ACT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g55730.1 Alt: ACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g55750.1 Alt: ACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.536; most accessible tissue: Callus, score: 85.874 |
| STR0433181362 (J) | chr04 | 33181362 | C | CTC | 96.00% | 0.00% | C -> CTC | NA |
|