6 variations found. LOC_Os05g11860 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 6,760,718 bp to 6,761,501 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0506760814 (J) | chr05 | 6760814 | T | G | 58.50% | 0.00% | G -> T |
mr1039 (All); LR P-value: 2.30E-26;
mr1514 (All); LR P-value: 4.43E-10; mr1632 (All); LR P-value: 3.19E-32; mr1873 (All); LR P-value: 1.22E-41; mr1039_2 (All); LR P-value: 8.15E-28; mr1517_2 (Jap_All); LR P-value: 2.16E-06; mr1632_2 (All); LR P-value: 4.82E-40; mr1722_2 (All); LR P-value: 9.57E-12; mr1748_2 (All); LR P-value: 2.47E-07; mr1873_2 (All); LR P-value: 5.76E-32; mr1973_2 (Jap_All); LMM P-value: 1.07E-07; LR P-value: 1.07E-07 |
LOC_Os05g11860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.233; most accessible tissue: Zhenshan97 young leaf, score: 81.353 |
| vg0506760956 (J) | chr05 | 6760956 | A | G | 52.10% | 0.08% | G -> A |
mr1039 (All); LR P-value: 1.86E-26;
mr1329 (All); LR P-value: 1.34E-13; mr1524 (All); LR P-value: 4.56E-10; mr1632 (All); LR P-value: 1.44E-27; mr1632 (Ind_All); LR P-value: 7.74E-06; mr1873 (All); LMM P-value: 8.10E-06; mr1039_2 (All); LR P-value: 1.43E-30; mr1514_2 (All); LMM P-value: 7.06E-07; LR P-value: 7.56E-19; mr1632_2 (All); LMM P-value: 1.90E-07; LR P-value: 4.85E-38; mr1632_2 (Ind_All); LR P-value: 1.00E-08 |
LOC_Os05g11860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g11860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.968; most accessible tissue: Zhenshan97 young leaf, score: 87.993 |
| vg0506760968 (J) | chr05 | 6760968 | A | C | 58.40% | 0.08% | C -> A |
mr1039 (All); LR P-value: 1.72E-26;
mr1514 (All); LR P-value: 9.33E-10; mr1632 (All); LR P-value: 4.22E-32; mr1873 (All); LR P-value: 2.82E-42; mr1039_2 (All); LR P-value: 6.09E-28; mr1632_2 (All); LR P-value: 3.01E-40; mr1722_2 (All); LR P-value: 8.05E-12; mr1748_2 (All); LR P-value: 3.27E-07; mr1873_2 (All); LR P-value: 3.81E-32 |
LOC_Os05g11860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g11860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.189; most accessible tissue: Zhenshan97 young leaf, score: 87.153 |
| vg0506761401 (J) | chr05 | 6761401 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os05g11860.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 83.117; most accessible tissue: Zhenshan97 young leaf, score: 92.231 |
| vg0506761454 (J) | chr05 | 6761454 | G | A | 97.80% | 0.00% | G -> A | NA |
LOC_Os05g11860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.246; most accessible tissue: Zhenshan97 young leaf, score: 92.356 |
| STR0506760963 (J) | chr05 | 6760963 | CGCCGAG | CGCCGCG | 53.40% | 0.00% | CGCCGCG -> CGCCGAG | NA |
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