48 variations found. LOC_Os02g45390 (RING-H2 finger protein; putative; expressed), ranging from 27,602,319 bp to 27,606,781 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0227604881 (J) | chr02 | 27604881 | TT | TTT | 97.30% | 0.00% | TT -> TTT | NA |
|
| vg0227602519 (J) | chr02 | 27602519 | AGTTT | ATT | 39.30% | 1.78% | AGTTT -> ATT,AT,ATT T,A | NA |
LOC_Os02g45390.1 Alt: ATT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g45390.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g45390.1 Alt: ATTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g45390.1 Alt: AT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.297; most accessible tissue: Minghui63 root, score: 97.144 |
| vg0227602520 (J) | chr02 | 27602520 | GT | TT | 40.40% | 54.82% | GT -> TT,GTT,G | NA |
LOC_Os02g45390.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g45390.1 Alt: TT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g45390.1 Alt: GTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.297; most accessible tissue: Minghui63 root, score: 97.144 |
| vg0227602521 (J) | chr02 | 27602521 | T | A | 92.10% | 1.48% | T -> A | NA |
LOC_Os02g45390.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.367; most accessible tissue: Minghui63 root, score: 97.188 |
| vg0227602522 (J) | chr02 | 27602522 | T | TCAA | 54.10% | 37.75% | T -> TCAA | NA |
LOC_Os02g45390.1 Alt: TCAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.367; most accessible tissue: Minghui63 root, score: 97.188 |
| vg0227602685 (J) | chr02 | 27602685 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os02g45390.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.300; most accessible tissue: Minghui63 flower, score: 94.526 |
| vg0227602847 (J) | chr02 | 27602847 | A | T | 99.40% | 0.00% | A -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.839; most accessible tissue: Minghui63 flower, score: 90.888 |
| vg0227602882 (J) | chr02 | 27602882 | G | A | 94.00% | 0.00% | G -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 81.888; most accessible tissue: Minghui63 flower, score: 89.033 |
| vg0227603011 (J) | chr02 | 27603011 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.167; most accessible tissue: Minghui63 flower, score: 82.109 |
| vg0227603012 (J) | chr02 | 27603012 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.277; most accessible tissue: Minghui63 flower, score: 82.244 |
| vg0227603022 (J) | chr02 | 27603022 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.806; most accessible tissue: Minghui63 flower, score: 82.891 |
| vg0227603024 (J) | chr02 | 27603024 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.737; most accessible tissue: Minghui63 flower, score: 82.891 |
| vg0227603055 (J) | chr02 | 27603055 | TA | T | 46.10% | 26.01% | TA -> TAA,T | NA |
LOC_Os02g45390.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 65.592; most accessible tissue: Callus, score: 78.441 |
| vg0227603064 (J) | chr02 | 27603064 | AAAC | A | 77.80% | 5.23% | AAAC -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 65.136; most accessible tissue: Callus, score: 78.441 |
| vg0227603065 (J) | chr02 | 27603065 | A | AAC | 51.30% | 0.00% | AAC -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 65.221; most accessible tissue: Callus, score: 78.441 |
| vg0227603067 (J) | chr02 | 27603067 | C | A | 98.50% | 0.00% | C -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 65.276; most accessible tissue: Callus, score: 78.441 |
| vg0227603112 (J) | chr02 | 27603112 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.004; most accessible tissue: Minghui63 flower, score: 71.756 |
| vg0227603329 (J) | chr02 | 27603329 | TGG | TG | 20.00% | 58.40% | TGG -> T,TG,TGGGG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g45390.1 Alt: TG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g45390.1 Alt: TGGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.186; most accessible tissue: Minghui63 flower, score: 67.440 |
| vg0227603336 (J) | chr02 | 27603336 | GA | G | 60.70% | 0.00% | G -> GA,A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g45390.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.938; most accessible tissue: Minghui63 flower, score: 66.684 |
| vg0227603361 (J) | chr02 | 27603361 | G | A | 93.70% | 0.00% | G -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 45.259; most accessible tissue: Minghui63 flower, score: 67.808 |
| vg0227603365 (J) | chr02 | 27603365 | T | C | 53.60% | 0.00% | C -> T |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 45.197; most accessible tissue: Minghui63 flower, score: 67.808 |
|
| vg0227603478 (J) | chr02 | 27603478 | T | A | 60.60% | 0.00% | A -> T |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 40.601; most accessible tissue: Callus, score: 69.199 |
|
| vg0227603617 (J) | chr02 | 27603617 | A | G | 60.60% | 0.02% | G -> A | NA |
LOC_Os02g45390.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 33.661; most accessible tissue: Callus, score: 47.032 |
| vg0227603681 (J) | chr02 | 27603681 | G | T | 99.50% | 0.00% | G -> T | NA |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 34.315; most accessible tissue: Callus, score: 66.928 |
| vg0227603832 (J) | chr02 | 27603832 | T | C | 53.50% | 0.04% | C -> T |
LOC_Os02g45390.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 34.976; most accessible tissue: Minghui63 flower, score: 51.629 |
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