5 variations found. LOC_Os04g49394 (ulp1 protease family; C-terminal catalytic domain containing protein; expressed), ranging from 29,480,742 bp to 29,481,057 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0429480824 (J) | chr04 | 29480824 | A | G | 56.50% | 0.36% | G -> A |
mr1051 (All); LR P-value: 2.17E-21;
mr1076 (Ind_All); LR P-value: 3.41E-06; mr1103 (Ind_All); LR P-value: 4.25E-06; mr1104 (Ind_All); LR P-value: 9.73E-06; mr1156 (All); LR P-value: 5.04E-15; mr1169 (All); LR P-value: 4.91E-12; mr1253 (All); LR P-value: 1.16E-18; mr1316 (All); LR P-value: 2.98E-10; mr1342 (All); LR P-value: 4.67E-09; mr1560 (Ind_All); LR P-value: 5.37E-07; mr1620 (All); LR P-value: 5.42E-39; mr1666 (All); LR P-value: 1.57E-07; mr1671 (All); LR P-value: 9.88E-58; mr1689 (All); LR P-value: 7.93E-22; mr1819 (All); LR P-value: 9.73E-13; mr1938 (All); LR P-value: 1.41E-11; mr1253_2 (All); LR P-value: 4.56E-21; mr1666_2 (All); LR P-value: 8.80E-12 |
LOC_Os04g49394.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49394.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.747; most accessible tissue: Callus, score: 96.095 |
| vg0429480833 (J) | chr04 | 29480833 | A | G | 56.60% | 0.36% | G -> A |
mr1003 (All); LR P-value: 3.02E-21;
mr1010 (All); LR P-value: 1.45E-12; mr1051 (All); LR P-value: 2.59E-22; mr1053 (All); LR P-value: 1.00E-06; mr1076 (All); LR P-value: 2.78E-26; mr1076 (Ind_All); LR P-value: 3.41E-06; mr1083 (All); LR P-value: 4.00E-23; mr1103 (Ind_All); LR P-value: 4.25E-06; mr1104 (Ind_All); LR P-value: 9.73E-06; mr1156 (All); LR P-value: 1.08E-15; mr1169 (All); LR P-value: 7.62E-12; mr1179 (All); LR P-value: 2.06E-18; mr1253 (All); LR P-value: 1.48E-18; mr1316 (All); LR P-value: 1.11E-10; mr1342 (All); LR P-value: 1.07E-09; mr1379 (All); LR P-value: 1.92E-09; mr1560 (All); LR P-value: 1.04E-29; mr1560 (Ind_All); LR P-value: 5.37E-07; mr1620 (All); LR P-value: 5.32E-39; mr1663 (All); LR P-value: 2.70E-09; mr1671 (All); LR P-value: 2.59E-57; mr1689 (All); LR P-value: 7.10E-23; mr1700 (All); LR P-value: 5.27E-17; mr1819 (All); LR P-value: 8.85E-14; mr1878 (All); LR P-value: 6.44E-32; mr1938 (All); LR P-value: 2.92E-12; mr1253_2 (All); LR P-value: 5.16E-21 |
LOC_Os04g49394.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49394.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.756; most accessible tissue: Zhenshan97 young leaf, score: 87.584 |
| vg0429480850 (J) | chr04 | 29480850 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os04g49394.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g49410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.136; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
| vg0429480887 (J) | chr04 | 29480887 | ACTTTCT TTGTCCT | A | 99.50% | 0.00% | ACTTTCTTTG TCCT -> A | NA |
LOC_Os04g49394.1 Alt: A| frameshift_variant HIGH(snpEff)
The average chromatin accessibility score: 79.780; most accessible tissue: Zhenshan97 young leaf, score: 87.299 |
| vg0429481016 (J) | chr04 | 29481016 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os04g49394.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.998; most accessible tissue: Callus, score: 94.223 |