331 variations found. LOC_Os04g52020 (PHD-finger domain containing protein; putative; expressed), ranging from 30,888,155 bp to 30,903,920 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0430890374 (J) | chr04 | 30890374 | CCCCCCT | CTCCCCT | 91.60% | 0.00% | CCCCCCT -> CTCCCCT | NA |
|
| STR0430895249 (J) | chr04 | 30895249 | TT | TG | 89.50% | 0.00% | TT -> TG | NA |
|
| STR0430903856 (J) | chr04 | 30903856 | AAAA | AAAAA | 89.70% | 0.00% | AAAA -> AAA,AAAAA | NA |
|
| vg0430888343 (J) | chr04 | 30888343 | G | A | 82.20% | 0.00% | G -> A |
LOC_Os04g52020.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.291; most accessible tissue: Zhenshan97 flower, score: 94.016 |
|
| vg0430888411 (J) | chr04 | 30888411 | T | C | 96.40% | 0.00% | T -> C |
LOC_Os04g52020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.440; most accessible tissue: Zhenshan97 flower, score: 94.883 |
|
| vg0430888465 (J) | chr04 | 30888465 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os04g52020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.678; most accessible tissue: Zhenshan97 flower, score: 93.553 |
| vg0430888558 (J) | chr04 | 30888558 | A | G | 91.80% | 0.00% | A -> G | NA |
LOC_Os04g52020.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.445; most accessible tissue: Zhenshan97 flower, score: 93.675 |
| vg0430888783 (J) | chr04 | 30888783 | A | AT | 94.10% | 0.00% | A -> AT | NA |
The average chromatin accessibility score: 79.781; most accessible tissue: Zhenshan97 flower, score: 90.548
|
| vg0430888821 (J) | chr04 | 30888821 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os04g52020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.664; most accessible tissue: Zhenshan97 flower, score: 88.247 |
| vg0430889320 (J) | chr04 | 30889320 | GATTCTT TTAGGGA AATATGT CCAGA | G | 94.30% | 0.00% | GATTCTTTTA GGGAAATATG TCCAGA -> G | NA |
LOC_Os04g52020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 67.695; most accessible tissue: Zhenshan97 flower, score: 83.915 |
| vg0430889447 (J) | chr04 | 30889447 | C | T | 85.80% | 0.00% | C -> T | NA |
LOC_Os04g52020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.659; most accessible tissue: Zhenshan97 flower, score: 85.564 |
| vg0430889564 (J) | chr04 | 30889564 | T | C | 94.20% | 0.00% | T -> C | NA |
LOC_Os04g52020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 66.369; most accessible tissue: Zhenshan97 flower, score: 83.499 |
| vg0430889580 (J) | chr04 | 30889580 | A | ATT | 99.60% | 0.00% | A -> ATT | NA |
The average chromatin accessibility score: 62.369; most accessible tissue: Zhenshan97 flower, score: 82.359
|
| vg0430889603 (J) | chr04 | 30889603 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.640; most accessible tissue: Zhenshan97 flower, score: 82.236 |
| vg0430889681 (J) | chr04 | 30889681 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os04g52020.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.652; most accessible tissue: Zhenshan97 flower, score: 85.053 |
| vg0430889799 (J) | chr04 | 30889799 | A | G | 76.50% | 0.00% | G -> A |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.295; most accessible tissue: Zhenshan97 flower, score: 85.053 |
|
| vg0430889800 (J) | chr04 | 30889800 | T | C | 85.90% | 0.00% | T -> C | NA |
LOC_Os04g52020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.928; most accessible tissue: Callus, score: 85.000 |
| vg0430889808 (J) | chr04 | 30889808 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os04g52020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.557; most accessible tissue: Zhenshan97 flower, score: 85.141 |
| vg0430890017 (J) | chr04 | 30890017 | G | GT | 85.80% | 0.00% | G -> GT | NA |
The average chromatin accessibility score: 65.562; most accessible tissue: Callus, score: 81.668
|
| vg0430890190 (J) | chr04 | 30890190 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.029; most accessible tissue: Callus, score: 83.599 |
| vg0430890206 (J) | chr04 | 30890206 | C | A | 85.80% | 0.00% | C -> A | NA |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.155; most accessible tissue: Callus, score: 83.599 |
| vg0430890375 (J) | chr04 | 30890375 | C | T | 85.80% | 0.00% | C -> T | NA |
LOC_Os04g52020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 48.807; most accessible tissue: Callus, score: 69.412 |
| vg0430890564 (J) | chr04 | 30890564 | A | G | 91.80% | 0.00% | A -> G | NA |
LOC_Os04g52020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.613; most accessible tissue: Minghui63 flag leaf, score: 94.034 |
| vg0430890570 (J) | chr04 | 30890570 | T | A | 92.20% | 0.00% | T -> A | NA |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.260; most accessible tissue: Minghui63 flag leaf, score: 94.601 |
| vg0430890651 (J) | chr04 | 30890651 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g52020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.176; most accessible tissue: Minghui63 flag leaf, score: 95.859 |
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