12 variations found. Os05g0393900/LOC_Os05g32730 (tetratricopeptide-like helical; putative; expressed), ranging from 19,166,573 bp to 19,168,235 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g32730 | tetratricopeptide-like helical, putative, expressed; RAP ID: Os05g0393900; MSU ID: LOC_Os05g32730 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0519166607 (J) | chr05 | 19166607 | A | G | 70.00% | 0.00% | G -> A |
LOC_Os05g32730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 43.906; most accessible tissue: Zhenshan97 young leaf, score: 66.320 |
|
| vg0519166799 (J) | chr05 | 19166799 | G | A | 63.90% | 0.68% | G -> A |
mr1044 (All); LR P-value: 2.81E-06;
mr1044 (Ind_All); LR P-value: 6.22E-06; mr1199 (Ind_All); LR P-value: 8.48E-06; mr1301 (Jap_All); LR P-value: 2.63E-14; mr1410 (Jap_All); LR P-value: 2.80E-11; mr1482 (All); LR P-value: 5.52E-06; mr1518 (Jap_All); LR P-value: 2.35E-06; mr1676 (Jap_All); LR P-value: 2.51E-09; mr1769 (Jap_All); LR P-value: 1.40E-13; mr1830 (Ind_All); LR P-value: 4.41E-07; mr1951 (Jap_All); LR P-value: 2.04E-08; mr1131_2 (Ind_All); LR P-value: 8.56E-07; mr1199_2 (Ind_All); LR P-value: 1.85E-07; mr1325_2 (Ind_All); LR P-value: 3.35E-06; mr1333_2 (Ind_All); LR P-value: 5.09E-06; mr1410_2 (Jap_All); LR P-value: 1.84E-11; mr1482_2 (All); LR P-value: 3.71E-09; mr1482_2 (Ind_All); LR P-value: 1.53E-06; mr1498_2 (All); LR P-value: 6.20E-07; mr1676_2 (Jap_All); LR P-value: 4.84E-09; mr1763_2 (All); LR P-value: 2.35E-06; mr1769_2 (Jap_All); LR P-value: 6.87E-15; mr1830_2 (Ind_All); LR P-value: 4.37E-07; mr1846_2 (Ind_All); LR P-value: 5.99E-08 |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 52.865; most accessible tissue: Callus, score: 81.399 |
| vg0519167025 (J) | chr05 | 19167025 | C | A | 69.90% | 0.06% | A -> C |
mr1277 (All); LR P-value: 1.35E-09;
mr1301 (All); LMM P-value: 9.66E-06; mr1410 (All); LMM P-value: 3.75E-07; mr1676 (Jap_All); LR P-value: 1.49E-07; mr1733 (All); LR P-value: 7.45E-33; mr1410_2 (All); LMM P-value: 3.17E-07; mr1629_2 (Jap_All); LR P-value: 1.03E-06; mr1676_2 (Jap_All); LR P-value: 2.38E-07 |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 59.539; most accessible tissue: Callus, score: 81.032 |
| vg0519167030 (J) | chr05 | 19167030 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os05g32730.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os05g32720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.919; most accessible tissue: Callus, score: 81.032 |
| vg0519167151 (J) | chr05 | 19167151 | C | T | 70.00% | 0.06% | T -> C |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 62.225; most accessible tissue: Minghui63 flag leaf, score: 81.811 |
|
| vg0519167166 (J) | chr05 | 19167166 | C | T | 70.00% | 0.06% | T -> C |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 62.449; most accessible tissue: Minghui63 flag leaf, score: 80.786 |
|
| vg0519167363 (J) | chr05 | 19167363 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os05g32730.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os05g32720.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.572; most accessible tissue: Minghui63 flag leaf, score: 88.342 |
| vg0519167432 (J) | chr05 | 19167432 | C | T | 65.90% | 0.66% | C -> T |
mr1044 (Ind_All); LR P-value: 3.37E-06;
mr1482 (Ind_All); LR P-value: 5.80E-06; mr1525 (Ind_All); LR P-value: 9.53E-06; mr1830 (Ind_All); LR P-value: 1.10E-06; mr1131_2 (Ind_All); LR P-value: 1.12E-06; mr1199_2 (Ind_All); LR P-value: 5.66E-07; mr1325_2 (Ind_All); LR P-value: 2.36E-06; mr1482_2 (Ind_All); LR P-value: 7.40E-06 |
LOC_Os05g32730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.506; most accessible tissue: Minghui63 flag leaf, score: 91.207 |
| vg0519167492 (J) | chr05 | 19167492 | G | A | 63.90% | 0.66% | G -> A |
mr1039 (Ind_All); LR P-value: 1.99E-07;
mr1044 (All); LR P-value: 1.26E-06; mr1044 (Ind_All); LR P-value: 1.57E-06; mr1199 (Ind_All); LR P-value: 2.07E-06; mr1301 (Jap_All); LR P-value: 2.63E-14; mr1410 (Jap_All); LR P-value: 2.80E-11; mr1482 (All); LR P-value: 4.26E-06; mr1482 (Ind_All); LR P-value: 6.60E-06; mr1518 (Jap_All); LR P-value: 2.35E-06; mr1525 (Ind_All); LR P-value: 9.03E-06; mr1676 (Jap_All); LR P-value: 2.51E-09; mr1769 (Jap_All); LR P-value: 1.40E-13; mr1830 (Ind_All); LR P-value: 2.46E-07; mr1951 (Jap_All); LR P-value: 2.04E-08; mr1131_2 (Ind_All); LR P-value: 5.92E-06; mr1199_2 (Ind_All); LR P-value: 1.65E-06; mr1325_2 (Ind_All); LR P-value: 1.79E-06; mr1333_2 (Ind_All); LR P-value: 7.07E-06; mr1410_2 (Jap_All); LR P-value: 1.84E-11; mr1482_2 (All); LR P-value: 1.65E-08; mr1482_2 (Ind_All); LR P-value: 6.45E-06; mr1498_2 (All); LR P-value: 1.04E-06; mr1676_2 (Jap_All); LR P-value: 4.84E-09; mr1763_2 (All); LR P-value: 8.52E-06; mr1769_2 (Jap_All); LR P-value: 6.87E-15 |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.480; most accessible tissue: Minghui63 flag leaf, score: 93.714 |
| vg0519168002 (J) | chr05 | 19168002 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os05g32730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.754; most accessible tissue: Minghui63 flag leaf, score: 98.608 |
| vg0519168068 (J) | chr05 | 19168068 | G | T | 66.60% | 0.40% | T -> G | NA |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 95.729; most accessible tissue: Minghui63 flag leaf, score: 98.522 |
| vg0519168226 (J) | chr05 | 19168226 | A | G | 57.70% | 5.14% | G -> A | NA |
LOC_Os05g32730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g32730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 98.465; most accessible tissue: Zhenshan97 panicle, score: 99.165 |