10 variations found. Os01g0866000/LOC_Os01g64620 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 37,505,154 bp to 37,506,089 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g64620 | zinc finger, C3HC4 type domain containing protein, expressed; RAP ID: Os01g0866000; MSU ID: LOC_Os01g64620 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137505314 (J) | chr01 | 37505314 | TCGGCGG CGGCGGC CGCCGGC GCGTCGC CTGGTCC GGCTGGG CGCGTGT TGGAAGG CGGCG | T | 97.50% | 0.00% | TCGGCGGCGG CGGCCGCCGG CGCGTCGCCT GGTCCGGCTG GGCGCGTGTT GGAAGGCGGC G -> T | NA |
LOC_Os01g64620.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 90.584; most accessible tissue: Minghui63 root, score: 95.301 |
| vg0137505385 (J) | chr01 | 37505385 | G | A | 91.10% | 3.87% | G -> A | NA |
LOC_Os01g64620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.554; most accessible tissue: Minghui63 panicle, score: 95.218 |
| vg0137505628 (J) | chr01 | 37505628 | G | C | 49.90% | 4.95% | G -> C,A | NA |
LOC_Os01g64620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64620.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g64620.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.333; most accessible tissue: Minghui63 panicle, score: 95.282 |
| vg0137505701 (J) | chr01 | 37505701 | G | T | 56.50% | 3.22% | T -> G | NA |
LOC_Os01g64620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.680; most accessible tissue: Zhenshan97 panicle, score: 94.949 |
| vg0137505782 (J) | chr01 | 37505782 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g64620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 89.991; most accessible tissue: Zhenshan97 panicle, score: 93.845 |
| vg0137505826 (J) | chr01 | 37505826 | C | T | 81.40% | 3.91% | T -> C | NA |
LOC_Os01g64620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g64620.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.710; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0137505927 (J) | chr01 | 37505927 | T | TCA | 64.20% | 0.00% | TCA -> T | NA |
LOC_Os01g64620.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g64630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.438; most accessible tissue: Callus, score: 91.795 |
| vg0137505966 (J) | chr01 | 37505966 | T | C | 55.10% | 0.04% | T -> C |
mr1213 (All); LR P-value: 4.80E-32;
mr1583 (All); LR P-value: 4.96E-15; mr1592 (All); LR P-value: 1.55E-13; mr1717 (All); LR P-value: 9.19E-07; mr1770 (All); LR P-value: 7.50E-10; mr1215_2 (All); LR P-value: 1.75E-07; mr1218_2 (All); LR P-value: 2.18E-20; mr1352_2 (All); LR P-value: 3.32E-16; mr1538_2 (All); LMM P-value: 1.21E-06; mr1850_2 (All); LR P-value: 5.03E-13; mr1870_2 (Ind_All); LR P-value: 1.49E-06; mr1885_2 (All); LR P-value: 2.68E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g64620.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.190; most accessible tissue: Callus, score: 91.795 |
| vg0137506002 (J) | chr01 | 37506002 | GT | GTT | 64.30% | 0.00% | GTT -> GT,GTTT,G | NA |
LOC_Os01g64620.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g64630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64620.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64620.1 Alt: GTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.135; most accessible tissue: Callus, score: 91.795 |
| vg0137506082 (J) | chr01 | 37506082 | C | T | 64.50% | 0.00% | T -> C | NA |
LOC_Os01g64620.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g64630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64630.4 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.789; most accessible tissue: Minghui63 root, score: 86.064 |