16 variations found. LOC_Os02g07770 (Myb transcription factor; putative; expressed), ranging from 4,058,207 bp to 4,060,231 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0204058310 (J) | chr02 | 4058310 | C | T | 68.40% | 0.00% | C -> T |
LOC_Os02g07770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 60.529; most accessible tissue: Minghui63 panicle, score: 85.556 |
|
| vg0204058436 (J) | chr02 | 4058436 | C | T | 96.00% | 0.00% | C -> T | NA |
LOC_Os02g07770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.421; most accessible tissue: Minghui63 panicle, score: 87.238 |
| vg0204058642 (J) | chr02 | 4058642 | G | T | 99.20% | 0.00% | G -> T | NA |
LOC_Os02g07770.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 65.472; most accessible tissue: Minghui63 panicle, score: 88.893 |
| vg0204058900 (J) | chr02 | 4058900 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os02g07770.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.373; most accessible tissue: Zhenshan97 panicle, score: 77.482 |
| vg0204058910 (J) | chr02 | 4058910 | C | G | 98.20% | 0.00% | C -> G | NA |
LOC_Os02g07770.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 56.488; most accessible tissue: Zhenshan97 panicle, score: 76.605 |
| vg0204059008 (J) | chr02 | 4059008 | TGTAGTT ATGGTAA TAATTAA | T | 96.00% | 0.00% | TGTAGTTATG GTAATAATTA A -> T | NA |
LOC_Os02g07770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.034; most accessible tissue: Callus, score: 74.473 |
| vg0204059211 (J) | chr02 | 4059211 | T | G | 58.60% | 0.00% | T -> G | NA |
LOC_Os02g07770.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.632; most accessible tissue: Callus, score: 80.707 |
| vg0204059219 (J) | chr02 | 4059219 | TTGGTGC AA | ATGGTGC AA | 58.00% | 0.00% | TTGGTGCAA -> ATGGTGCAA, T | NA |
LOC_Os02g07770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g07770.1 Alt: ATGGTGCAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.858; most accessible tissue: Callus, score: 80.707 |
| vg0204059351 (J) | chr02 | 4059351 | A | G | 98.20% | 0.00% | A -> G | NA |
LOC_Os02g07770.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 39.750; most accessible tissue: Callus, score: 60.214 |
| vg0204059356 (J) | chr02 | 4059356 | G | T | 58.70% | 0.00% | G -> T | NA |
LOC_Os02g07770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 39.874; most accessible tissue: Callus, score: 60.214 |
| vg0204059402 (J) | chr02 | 4059402 | C | CA | 49.90% | 0.91% | C -> CA,CAA,CAA A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g07770.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g07770.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g07770.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.332; most accessible tissue: Callus, score: 60.214 |
| vg0204059404 (J) | chr02 | 4059404 | A | AC | 98.10% | 0.00% | A -> AC | NA |
The average chromatin accessibility score: 41.274; most accessible tissue: Callus, score: 60.214
|
| vg0204059521 (J) | chr02 | 4059521 | C | G | 98.30% | 0.00% | C -> G | NA |
LOC_Os02g07770.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 41.447; most accessible tissue: Callus, score: 81.190 |
| vg0204059647 (J) | chr02 | 4059647 | G | T | 98.30% | 0.00% | G -> T | NA |
LOC_Os02g07770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.628; most accessible tissue: Callus, score: 57.499 |
| vg0204059965 (J) | chr02 | 4059965 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os02g07770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 61.112; most accessible tissue: Minghui63 panicle, score: 85.556 |
| STR0204059646 (J) | chr02 | 4059646 | TG | TT | 98.20% | 0.00% | TG -> TT | NA |
|