9 variations found. LOC_Os01g67800 (retrotransposon protein; putative; unclassified; expressed), ranging from 39,403,150 bp to 39,407,485 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0139403190 (J) | chr01 | 39403190 | GGCGTCG TGCGCGG GGTGC | G | 29.20% | 68.96% | GGCGTCGTGC GCGGGGTGC -> G | NA |
LOC_Os01g67800.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.053; most accessible tissue: Zhenshan97 young leaf, score: 96.911 |
| vg0139403433 (J) | chr01 | 39403433 | G | A | 7.90% | 77.30% | G -> A | NA |
LOC_Os01g67800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0139403610 (J) | chr01 | 39403610 | C | T | 9.50% | 75.62% | C -> T | NA |
LOC_Os01g67800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0139404590 (J) | chr01 | 39404590 | G | A | 25.30% | 69.72% | G -> A | NA |
LOC_Os01g67800.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0139404672 (J) | chr01 | 39404672 | G | A | 29.20% | 68.58% | G -> A | NA |
LOC_Os01g67800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0139407120 (J) | chr01 | 39407120 | A | G | 29.60% | 53.11% | A -> G | NA |
LOC_Os01g67800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.802; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0139407180 (J) | chr01 | 39407180 | G | A | 30.90% | 54.34% | G -> A | NA |
LOC_Os01g67800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.934; most accessible tissue: Zhenshan97 flower, score: 19.041 |
| vg0139407380 (J) | chr01 | 39407380 | C | T | 20.20% | 72.03% | C -> T | NA |
LOC_Os01g67800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.604; most accessible tissue: Zhenshan97 flower, score: 31.800 |
| vg0139407423 (J) | chr01 | 39407423 | C | T | 20.40% | 71.60% | C -> T | NA |
LOC_Os01g67800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.141; most accessible tissue: Zhenshan97 flower, score: 32.793 |