17 variations found. Os06g0534900/LOC_Os06g34400 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 20,019,171 bp to 20,021,317 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os06g34400 | zinc finger, C3HC4 type domain containing protein, expressed; RAP ID: Os06g0534900; MSU ID: LOC_Os06g34400 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620019428 (J) | chr06 | 20019428 | C | T | 43.70% | 15.15% | C -> T | NA |
LOC_Os06g34400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.983; most accessible tissue: Minghui63 panicle, score: 98.225 |
| vg0620019499 (J) | chr06 | 20019499 | C | T | 40.90% | 16.78% | C -> T | NA |
LOC_Os06g34400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.543; most accessible tissue: Minghui63 panicle, score: 98.182 |
| vg0620019763 (J) | chr06 | 20019763 | C | T | 74.50% | 0.00% | T -> C | NA |
LOC_Os06g34400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.238; most accessible tissue: Minghui63 panicle, score: 98.004 |
| vg0620019930 (J) | chr06 | 20019930 | CCGCCGC CGT | C | 73.50% | 0.00% | C -> CCGCCGCCGT | NA |
The average chromatin accessibility score: 90.353; most accessible tissue: Minghui63 panicle, score: 98.182
|
| vg0620019937 (J) | chr06 | 20019937 | CGCGACG | C | 99.80% | 0.00% | CGCGACG -> C | NA |
LOC_Os06g34400.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)
The average chromatin accessibility score: 90.360; most accessible tissue: Minghui63 panicle, score: 98.182 |
| vg0620019938 (J) | chr06 | 20019938 | G | GT | 99.90% | 0.00% | G -> GT,GTCGC | NA |
The average chromatin accessibility score: 90.294; most accessible tissue: Minghui63 panicle, score: 98.151
|
| vg0620019941 (J) | chr06 | 20019941 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os06g34400.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 90.204; most accessible tissue: Minghui63 panicle, score: 98.119 |
| vg0620020001 (J) | chr06 | 20020001 | T | TTCACTA G | 92.50% | 0.00% | T -> TTCACTAG | NA |
LOC_Os06g34410.1 Alt: TTCACTAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34400.1 Alt: TTCACTAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.396; most accessible tissue: Zhenshan97 flower, score: 98.194 |
| vg0620020051 (J) | chr06 | 20020051 | A | C | 90.90% | 0.00% | A -> C | NA |
LOC_Os06g34410.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.752; most accessible tissue: Zhenshan97 flower, score: 98.410 |
| vg0620020067 (J) | chr06 | 20020067 | T | C | 66.00% | 0.00% | C -> T |
mr1059 (All); LR P-value: 1.01E-14;
mr1167 (All); LR P-value: 2.87E-16; mr1245 (All); LR P-value: 1.49E-07; mr1325 (All); LR P-value: 6.58E-11; mr1335 (All); LR P-value: 1.16E-12; mr1369 (All); LR P-value: 8.22E-07; mr1453 (All); LR P-value: 6.05E-07; mr1527 (All); LR P-value: 2.92E-06; mr1529 (All); LR P-value: 1.51E-17; mr1532 (All); LR P-value: 3.38E-06; mr1675 (All); LR P-value: 2.67E-15; mr1690 (All); LR P-value: 2.98E-07; mr1726 (All); LR P-value: 1.35E-14; mr1950 (All); LR P-value: 1.19E-16; mr1969 (All); LR P-value: 2.18E-14; mr1950_2 (All); LR P-value: 2.58E-14 |
LOC_Os06g34410.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34400.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.708; most accessible tissue: Zhenshan97 flower, score: 98.436 |
| vg0620020414 (J) | chr06 | 20020414 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os06g34410.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34400.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.387; most accessible tissue: Zhenshan97 flower, score: 98.816 |
| vg0620020513 (J) | chr06 | 20020513 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os06g34400.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g34410.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.207; most accessible tissue: Zhenshan97 flower, score: 98.859 |
| vg0620020536 (J) | chr06 | 20020536 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os06g34400.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g34410.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.096; most accessible tissue: Zhenshan97 flower, score: 98.673 |
| vg0620020790 (J) | chr06 | 20020790 | C | A | 67.90% | 11.15% | C -> A | NA |
LOC_Os06g34400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.147; most accessible tissue: Minghui63 panicle, score: 98.021 |
| vg0620020791 (J) | chr06 | 20020791 | A | G | 58.00% | 6.39% | G -> A | NA |
LOC_Os06g34400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.147; most accessible tissue: Minghui63 panicle, score: 98.021 |
| vg0620020799 (J) | chr06 | 20020799 | G | A | 41.30% | 14.52% | G -> A | NA |
LOC_Os06g34400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.222; most accessible tissue: Minghui63 panicle, score: 98.004 |
| vg0620020986 (J) | chr06 | 20020986 | C | T | 77.30% | 5.50% | C -> T | NA |
LOC_Os06g34400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.056; most accessible tissue: Minghui63 panicle, score: 98.296 |