14 variations found. Os01g0868800/LOC_Os01g64850 (OsSub10 - Putative Subtilisin homologue; expressed), ranging from 37,647,018 bp to 37,649,292 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g64850 | OsSub10 - Putative Subtilisin homologue; RAP ID: Os01g0868800; MSU ID: LOC_Os01g64850 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137647054 (J) | chr01 | 37647054 | G | T | 64.50% | 0.17% | T -> G | NA |
LOC_Os01g64850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.839; most accessible tissue: Callus, score: 91.286 |
| vg0137647192 (J) | chr01 | 37647192 | G | A | 88.80% | 0.00% | G -> A |
mr1078 (Ind_All); LR P-value: 7.40E-10;
mr1144 (Ind_All); LR P-value: 1.12E-07; mr1244 (Ind_All); LR P-value: 1.05E-08; mr1068_2 (Ind_All); LR P-value: 4.30E-09; mr1078_2 (Ind_All); LR P-value: 1.15E-08; mr1112_2 (Ind_All); LR P-value: 6.48E-09; mr1144_2 (Ind_All); LR P-value: 1.70E-06; mr1200_2 (Ind_All); LR P-value: 8.32E-09; mr1244_2 (Ind_All); LR P-value: 4.35E-07; mr1870_2 (Ind_All); LR P-value: 1.82E-06 |
LOC_Os01g64850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.071; most accessible tissue: Minghui63 flag leaf, score: 88.907 |
| vg0137647407 (J) | chr01 | 37647407 | C | T | 83.40% | 0.00% | C -> T |
mr1066 (All); LR P-value: 1.81E-06;
mr1078 (Ind_All); LR P-value: 7.40E-10; mr1144 (Ind_All); LR P-value: 1.12E-07; mr1244 (All); LR P-value: 3.48E-20; mr1244 (Ind_All); LR P-value: 1.05E-08; mr1887 (All); LR P-value: 5.67E-06; mr1951 (All); LR P-value: 9.95E-07; mr1068_2 (Ind_All); LR P-value: 4.30E-09; mr1078_2 (Ind_All); LR P-value: 1.15E-08; mr1112_2 (Ind_All); LR P-value: 6.48E-09; mr1144_2 (Ind_All); LR P-value: 1.70E-06; mr1200_2 (Ind_All); LR P-value: 8.32E-09; mr1244_2 (Ind_All); LR P-value: 4.35E-07; mr1870_2 (Ind_All); LR P-value: 1.82E-06 |
LOC_Os01g64850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 82.189; most accessible tissue: Zhenshan97 flag leaf, score: 90.894 |
| vg0137647427 (J) | chr01 | 37647427 | G | C | 98.80% | 0.00% | G -> C | NA |
LOC_Os01g64850.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g64860.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g64840.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.245; most accessible tissue: Zhenshan97 flag leaf, score: 91.286 |
| vg0137647569 (J) | chr01 | 37647569 | C | T | 94.40% | 0.00% | T -> C |
LOC_Os01g64850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.540; most accessible tissue: Zhenshan97 flag leaf, score: 90.791 |
|
| vg0137647576 (J) | chr01 | 37647576 | G | A | 99.30% | 0.00% | G -> C,A | NA |
LOC_Os01g64850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 80.853; most accessible tissue: Zhenshan97 flag leaf, score: 90.738 |
| vg0137647760 (J) | chr01 | 37647760 | C | A | 64.50% | 0.00% | A -> C | NA |
LOC_Os01g64850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.319; most accessible tissue: Zhenshan97 flag leaf, score: 90.631 |
| vg0137647852 (J) | chr01 | 37647852 | G | C | 94.60% | 0.00% | G -> C |
mr1099 (All); LR P-value: 7.39E-27;
mr1113 (All); LR P-value: 5.20E-16; mr1114 (All); LR P-value: 2.16E-19; mr1117 (All); LR P-value: 9.50E-21; mr1119 (All); LR P-value: 5.45E-17; mr1120 (All); LR P-value: 8.30E-21; mr1123 (All); LR P-value: 3.35E-25; mr1158 (All); LR P-value: 5.05E-15; mr1168 (All); LR P-value: 8.28E-22; mr1240 (All); LR P-value: 4.23E-16; mr1247 (All); LR P-value: 6.03E-22; mr1365 (All); LR P-value: 2.99E-06; mr1496 (All); LR P-value: 1.08E-15; mr1550 (All); LR P-value: 5.99E-41; mr1612 (All); LR P-value: 4.75E-13; mr1757 (All); LR P-value: 5.81E-37; mr1774 (All); LR P-value: 8.14E-06; mr1936 (All); LR P-value: 4.78E-18; mr1989 (All); LR P-value: 1.15E-07; mr1113_2 (All); LR P-value: 1.88E-17; mr1114_2 (All); LR P-value: 2.02E-17; mr1117_2 (All); LR P-value: 1.80E-19; mr1119_2 (All); LR P-value: 1.74E-17; mr1120_2 (All); LR P-value: 1.60E-22; mr1123_2 (All); LR P-value: 5.86E-23; mr1247_2 (All); LR P-value: 9.01E-24; mr1496_2 (All); LR P-value: 4.23E-13; mr1549_2 (All); LR P-value: 5.46E-31; mr1550_2 (All); LR P-value: 4.58E-47; mr1757_2 (All); LR P-value: 1.81E-26 |
LOC_Os01g64850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.926; most accessible tissue: Zhenshan97 flag leaf, score: 90.123 |
| vg0137647964 (J) | chr01 | 37647964 | C | A | 83.40% | 0.00% | C -> A |
mr1066 (All); LR P-value: 1.81E-06;
mr1078 (Ind_All); LR P-value: 7.40E-10; mr1144 (Ind_All); LR P-value: 1.12E-07; mr1244 (All); LR P-value: 3.48E-20; mr1244 (Ind_All); LR P-value: 1.05E-08; mr1887 (All); LR P-value: 5.67E-06; mr1951 (All); LR P-value: 9.95E-07; mr1068_2 (Ind_All); LR P-value: 4.30E-09; mr1078_2 (Ind_All); LR P-value: 1.15E-08; mr1112_2 (Ind_All); LR P-value: 6.48E-09; mr1144_2 (Ind_All); LR P-value: 1.70E-06; mr1200_2 (Ind_All); LR P-value: 8.32E-09; mr1244_2 (Ind_All); LR P-value: 4.35E-07; mr1870_2 (Ind_All); LR P-value: 1.82E-06 |
LOC_Os01g64850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.239; most accessible tissue: Zhenshan97 flag leaf, score: 87.755 |
| vg0137648017 (J) | chr01 | 37648017 | C | T | 96.30% | 0.00% | C -> T | NA |
LOC_Os01g64850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.823; most accessible tissue: Zhenshan97 flag leaf, score: 86.884 |
| vg0137648052 (J) | chr01 | 37648052 | C | T | 64.40% | 0.00% | T -> C | NA |
LOC_Os01g64850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 80.476; most accessible tissue: Zhenshan97 flag leaf, score: 87.567 |
| vg0137648491 (J) | chr01 | 37648491 | G | T | 64.40% | 0.02% | T -> G | NA |
LOC_Os01g64850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.984; most accessible tissue: Zhenshan97 young leaf, score: 85.364 |
| vg0137648674 (J) | chr01 | 37648674 | A | G | 64.40% | 0.00% | G -> A | NA |
LOC_Os01g64850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.689; most accessible tissue: Zhenshan97 young leaf, score: 85.364 |
| vg0137648693 (J) | chr01 | 37648693 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os01g64850.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g64860.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.230; most accessible tissue: Zhenshan97 young leaf, score: 85.715 |