21 variations found. Os01g0820000/LOC_Os01g60450 (cytochrome P450; putative; expressed), ranging from 34,961,975 bp to 34,963,642 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g60450 | cytochrome P450, putative; RAP ID: Os01g0820000; MSU ID: LOC_Os01g60450 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0134962038 (J) | chr01 | 34962038 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g60450.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g60440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g60460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.160; most accessible tissue: Zhenshan97 flag leaf, score: 90.685 |
| vg0134962057 (J) | chr01 | 34962057 | G | A | 98.90% | 0.00% | G -> A |
LOC_Os01g60450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.372; most accessible tissue: Zhenshan97 flag leaf, score: 91.143 |
|
| vg0134962215 (J) | chr01 | 34962215 | G | T | 60.20% | 0.00% | T -> G |
mr1008 (All); LMM P-value: 1.42E-09;
mr1009 (All); LMM P-value: 9.26E-10; mr1538 (All); LR P-value: 3.74E-66; mr1580 (All); LR P-value: 2.44E-20; mr1825 (All); LR P-value: 5.21E-17; mr1008_2 (All); LMM P-value: 2.99E-10; mr1133_2 (All); LR P-value: 6.70E-15; mr1151_2 (All); LR P-value: 3.31E-13; mr1298_2 (All); LR P-value: 1.44E-21; mr1698_2 (All); LR P-value: 4.27E-22; mr1731_2 (All); LR P-value: 1.11E-20; mr1825_2 (All); LR P-value: 6.99E-29; mr1922_2 (All); LR P-value: 1.38E-19; mr1940_2 (All); LR P-value: 1.45E-08; mr1950_2 (All); LR P-value: 5.85E-15 |
LOC_Os01g60450.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.452; most accessible tissue: Zhenshan97 flag leaf, score: 89.490 |
| vg0134962399 (J) | chr01 | 34962399 | C | G | 60.20% | 0.00% | G -> C |
mr1008 (All); LMM P-value: 1.42E-09;
mr1009 (All); LMM P-value: 9.26E-10; mr1538 (All); LR P-value: 3.74E-66; mr1580 (All); LR P-value: 2.44E-20; mr1825 (All); LR P-value: 5.21E-17; mr1008_2 (All); LMM P-value: 2.99E-10; mr1133_2 (All); LR P-value: 6.70E-15; mr1151_2 (All); LR P-value: 3.31E-13; mr1298_2 (All); LR P-value: 1.44E-21; mr1698_2 (All); LR P-value: 4.27E-22; mr1731_2 (All); LR P-value: 1.11E-20; mr1825_2 (All); LR P-value: 6.99E-29; mr1922_2 (All); LR P-value: 1.38E-19; mr1940_2 (All); LR P-value: 1.45E-08; mr1950_2 (All); LR P-value: 5.85E-15 |
LOC_Os01g60450.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.790; most accessible tissue: Zhenshan97 flag leaf, score: 90.685 |
| vg0134962403 (J) | chr01 | 34962403 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os01g60450.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g60440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g60460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.735; most accessible tissue: Zhenshan97 flag leaf, score: 90.577 |
| vg0134962425 (J) | chr01 | 34962425 | G | A | 88.50% | 0.00% | G -> A |
LOC_Os01g60450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.904; most accessible tissue: Zhenshan97 flag leaf, score: 89.753 |
|
| vg0134962480 (J) | chr01 | 34962480 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os01g60450.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g60440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g60460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.465; most accessible tissue: Zhenshan97 flag leaf, score: 89.753 |
| vg0134962630 (J) | chr01 | 34962630 | G | T | 60.30% | 0.00% | T -> G |
mr1008 (All); LMM P-value: 1.93E-07;
mr1009 (All); LMM P-value: 9.78E-08; mr1416 (All); LR P-value: 2.01E-21; mr1538 (All); LR P-value: 5.97E-70; mr1541 (All); LR P-value: 1.37E-19; mr1580 (All); LR P-value: 2.21E-20; mr1713 (All); LR P-value: 6.10E-11; mr1825 (All); LR P-value: 1.15E-17; mr1008_2 (All); LMM P-value: 7.50E-07; mr1151_2 (All); LR P-value: 1.55E-13; mr1298_2 (All); LR P-value: 2.72E-21; mr1558_2 (All); LR P-value: 3.17E-57; mr1698_2 (All); LR P-value: 6.82E-22; mr1731_2 (All); LR P-value: 1.67E-20; mr1825_2 (All); LR P-value: 1.95E-29; mr1922_2 (All); LR P-value: 2.50E-20; mr1940_2 (All); LR P-value: 1.62E-08; mr1950_2 (All); LR P-value: 3.38E-14 |
LOC_Os01g60440.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60460.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60450.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.906; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 |
| vg0134962633 (J) | chr01 | 34962633 | C | G | 99.10% | 0.00% | C -> G | NA |
LOC_Os01g60440.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g60460.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60450.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.527; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 |
| vg0134962827 (J) | chr01 | 34962827 | A | G | 55.60% | 0.21% | A -> G |
mr1003 (All); LR P-value: 8.26E-25;
mr1003 (Ind_All); LR P-value: 3.57E-06; mr1008 (Ind_All); LMM P-value: 9.24E-06; LR P-value: 1.11E-06; mr1009 (All); LMM P-value: 8.46E-06; mr1009 (Ind_All); LMM P-value: 2.15E-06; LR P-value: 3.78E-06; mr1051 (All); LR P-value: 1.04E-23; mr1457 (All); LR P-value: 1.50E-09; mr1527 (All); LR P-value: 7.46E-07; mr1580 (All); LR P-value: 1.63E-19; mr1727 (All); LR P-value: 4.08E-07; mr1887 (Ind_All); LR P-value: 4.95E-06; mr1008_2 (Ind_All); LMM P-value: 6.80E-07; LR P-value: 1.29E-07; mr1027_2 (Ind_All); LR P-value: 2.26E-08; mr1051_2 (All); LR P-value: 6.60E-27; mr1051_2 (Ind_All); LR P-value: 6.89E-06; mr1218_2 (All); LR P-value: 1.19E-18; mr1244_2 (All); LR P-value: 1.79E-26; mr1850_2 (All); LR P-value: 1.37E-11 |
LOC_Os01g60440.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60460.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60450.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.307; most accessible tissue: Minghui63 flower, score: 85.573 |
| vg0134962845 (J) | chr01 | 34962845 | G | A | 88.30% | 0.23% | G -> A |
LOC_Os01g60440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60450.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 72.671; most accessible tissue: Minghui63 flag leaf, score: 85.151 |
|
| vg0134962955 (J) | chr01 | 34962955 | T | C | 51.70% | 0.21% | T -> C |
mr1003 (All); LR P-value: 2.10E-21;
mr1003 (Ind_All); LR P-value: 1.20E-06; mr1008 (Ind_All); LR P-value: 8.25E-06; mr1051 (Ind_All); LR P-value: 7.82E-06; mr1580 (All); LR P-value: 2.48E-20; mr1887 (Ind_All); LR P-value: 2.67E-06; mr1008_2 (All); LMM P-value: 9.31E-06; mr1008_2 (Ind_All); LMM P-value: 6.20E-08; LR P-value: 1.13E-07; mr1027_2 (Ind_All); LR P-value: 1.02E-08; mr1051_2 (Ind_All); LR P-value: 6.36E-06; mr1335_2 (All); LR P-value: 1.05E-07; mr1553_2 (All); LR P-value: 1.76E-12 |
LOC_Os01g60450.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g60450.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 77.274; most accessible tissue: Minghui63 flag leaf, score: 87.980 |
| vg0134962972 (J) | chr01 | 34962972 | GCGGAGG ATGGGGA TGAAGT | G | 91.90% | 0.23% | GCGGAGGATG GGGATGAAGT -> G | NA |
LOC_Os01g60450.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g60450.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.027; most accessible tissue: Minghui63 flag leaf, score: 87.326 |
| vg0134963074 (J) | chr01 | 34963074 | C | T | 51.70% | 0.00% | C -> T |
mr1003 (All); LR P-value: 4.47E-21;
mr1003 (Ind_All); LR P-value: 5.42E-06; mr1008 (Ind_All); LR P-value: 1.81E-06; mr1009 (Ind_All); LMM P-value: 4.78E-06; LR P-value: 7.93E-06; mr1527 (All); LR P-value: 5.27E-07; mr1580 (All); LR P-value: 6.59E-21; mr1887 (Ind_All); LR P-value: 7.19E-06; mr1008_2 (Ind_All); LMM P-value: 5.59E-06; LR P-value: 5.33E-07; mr1027_2 (Ind_All); LR P-value: 1.25E-08; mr1051_2 (Ind_All); LR P-value: 7.36E-06; mr1335_2 (All); LR P-value: 4.46E-08; mr1553_2 (All); LR P-value: 1.99E-12 |
LOC_Os01g60450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.581; most accessible tissue: Minghui63 flag leaf, score: 89.621 |
| vg0134963117 (J) | chr01 | 34963117 | T | C | 60.20% | 0.00% | C -> T |
mr1008 (All); LMM P-value: 1.03E-08;
mr1009 (All); LMM P-value: 1.35E-08; mr1040 (All); LR P-value: 8.11E-07; mr1580 (All); LR P-value: 1.49E-19; mr1008_2 (All); LMM P-value: 4.30E-10; mr1015_2 (All); LMM P-value: 6.76E-06; mr1133_2 (All); LR P-value: 8.59E-15; mr1151_2 (All); LR P-value: 1.10E-12; mr1298_2 (All); LR P-value: 6.76E-21; mr1731_2 (All); LR P-value: 3.60E-20; mr1940_2 (All); LR P-value: 2.48E-08 |
LOC_Os01g60450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.640; most accessible tissue: Minghui63 flag leaf, score: 91.758 |
| vg0134963133 (J) | chr01 | 34963133 | G | A | 51.80% | 0.00% | G -> A |
mr1003 (Ind_All); LR P-value: 4.91E-06;
mr1008 (Ind_All); LMM P-value: 2.57E-06; LR P-value: 4.01E-07; mr1009 (Ind_All); LMM P-value: 2.01E-06; LR P-value: 3.25E-06; mr1527 (All); LR P-value: 6.80E-07; mr1580 (All); LR P-value: 5.71E-20; mr1008_2 (All); LMM P-value: 4.08E-06; mr1008_2 (Ind_All); LMM P-value: 4.39E-07; LR P-value: 6.05E-08; mr1027_2 (Ind_All); LR P-value: 1.01E-10; mr1051_2 (Ind_All); LR P-value: 2.54E-06; mr1335_2 (All); LR P-value: 3.75E-08; mr1553_2 (All); LR P-value: 3.95E-12 |
LOC_Os01g60450.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g60440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.388; most accessible tissue: Minghui63 flag leaf, score: 91.625 |
| vg0134963165 (J) | chr01 | 34963165 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os01g60450.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g60440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.955; most accessible tissue: Minghui63 flag leaf, score: 92.689 |
| vg0134963182 (J) | chr01 | 34963182 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os01g60450.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g60440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g60460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.302; most accessible tissue: Minghui63 flag leaf, score: 92.527 |
| vg0134963295 (J) | chr01 | 34963295 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os01g60450.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os01g60440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g60460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.865; most accessible tissue: Minghui63 flag leaf, score: 93.043 |
| vg0134963402 (J) | chr01 | 34963402 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g60450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.757; most accessible tissue: Zhenshan97 young leaf, score: 93.371 |
| vg0134963634 (J) | chr01 | 34963634 | G | T | 92.20% | 0.00% | G -> T |
LOC_Os01g60450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.890; most accessible tissue: Zhenshan97 young leaf, score: 96.964 |