112 variations found. LOC_Os12g43660 (receptor-like protein kinase HAIKU2 precursor; putative; expressed), ranging from 27,122,485 bp to 27,126,252 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR1227122608 (J) | chr12 | 27122608 | AACAACA ACA | AACAACA ACAACAA | 47.30% | 0.00% | AACAACAACA -> AACAACAACA ACAA | NA |
|
| STR1227122619 (J) | chr12 | 27122619 | AAGAAG | AAGAAGA AGA | 47.00% | 0.00% | AAGAAG -> AAGAAGAAGA | NA |
|
| STR1227124797 (J) | chr12 | 27124797 | GGCGGCG G | GGCGGCG GCGG | 46.50% | 0.00% | GGCGGCGGCG G -> GGCGGCGG | NA |
|
| STR1227125807 (J) | chr12 | 27125807 | AC | AT | 46.10% | 0.00% | AC -> AT | NA |
|
| vg1227122507 (J) | chr12 | 27122507 | TCA | T | 96.80% | 0.00% | TCA -> T | NA |
LOC_Os12g43660.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 94.519; most accessible tissue: Zhenshan97 panicle, score: 97.869 |
| vg1227122528 (J) | chr12 | 27122528 | C | T | 54.70% | 0.61% | C -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g43660.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.972; most accessible tissue: Zhenshan97 panicle, score: 97.598 |
|
| vg1227122539 (J) | chr12 | 27122539 | T | G | 54.70% | 0.61% | T -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g43660.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.744; most accessible tissue: Zhenshan97 panicle, score: 97.512 |
|
| vg1227122540 (J) | chr12 | 27122540 | C | T | 54.70% | 0.61% | C -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g43660.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.681; most accessible tissue: Zhenshan97 panicle, score: 97.468 |
|
| vg1227122550 (J) | chr12 | 27122550 | AACACT | A | 55.00% | 0.61% | AACACT -> A,AACACTAC ACT | NA |
LOC_Os12g43660.1 Alt: AACACTACACT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g43660.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 93.468; most accessible tissue: Zhenshan97 panicle, score: 97.376 |
| vg1227122593 (J) | chr12 | 27122593 | ATAC | A | 54.70% | 0.55% | ATAC -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g43660.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.331; most accessible tissue: Zhenshan97 panicle, score: 96.702 |
| vg1227122596 (J) | chr12 | 27122596 | C | CATA | 99.80% | 0.00% | C -> CATA | NA |
The average chromatin accessibility score: 89.225; most accessible tissue: Zhenshan97 panicle, score: 96.563
|
| vg1227122620 (J) | chr12 | 27122620 | A | AGATC | 54.70% | 0.55% | A -> AGATC | NA |
LOC_Os12g43660.1 Alt: AGATC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.825; most accessible tissue: Zhenshan97 panicle, score: 96.087 |
| vg1227122700 (J) | chr12 | 27122700 | A | ACCT | 54.80% | 0.66% | A -> ACCT | NA |
LOC_Os12g43660.1 Alt: ACCT| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.290; most accessible tissue: Minghui63 panicle, score: 92.380 |
| vg1227122701 (J) | chr12 | 27122701 | T | C | 87.40% | 2.62% | T -> C |
LOC_Os12g43660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.255; most accessible tissue: Minghui63 panicle, score: 92.380 |
|
| vg1227122702 (J) | chr12 | 27122702 | C | G | 55.00% | 0.66% | C -> G | NA |
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g43660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os12g43660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.284; most accessible tissue: Minghui63 panicle, score: 92.380 |
| vg1227122705 (J) | chr12 | 27122705 | C | G | 99.40% | 0.00% | C -> G | NA |
LOC_Os12g43660.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 86.211; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg1227122708 (J) | chr12 | 27122708 | G | C | 99.40% | 0.00% | G -> C | NA |
LOC_Os12g43660.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 86.345; most accessible tissue: Minghui63 panicle, score: 92.526 |
| vg1227122711 (J) | chr12 | 27122711 | G | C | 54.90% | 0.66% | G -> C,GTTC |
LOC_Os12g43660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g43660.1 Alt: GTTC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 86.109; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
|
| vg1227122726 (J) | chr12 | 27122726 | T | C | 58.70% | 29.62% | T -> C | NA |
LOC_Os12g43660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.000; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg1227122730 (J) | chr12 | 27122730 | GTCGTCT TCT | G | 54.70% | 0.55% | GTCGTCTTCT -> G | NA |
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g43660.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 85.812; most accessible tissue: Zhenshan97 panicle, score: 91.992 |
| vg1227122762 (J) | chr12 | 27122762 | G | T | 54.70% | 0.49% | G -> T |
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g43660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.127; most accessible tissue: Minghui63 panicle, score: 91.756 |
|
| vg1227122764 (J) | chr12 | 27122764 | T | C | 54.70% | 0.49% | T -> C |
LOC_Os12g43660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.409; most accessible tissue: Minghui63 panicle, score: 91.756 |
|
| vg1227122859 (J) | chr12 | 27122859 | G | T | 54.60% | 0.70% | G -> T |
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g43660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 82.756; most accessible tissue: Minghui63 panicle, score: 91.410 |
|
| vg1227122866 (J) | chr12 | 27122866 | C | G | 54.60% | 0.70% | C -> G |
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g43660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 82.780; most accessible tissue: Minghui63 panicle, score: 91.034 |
|
| vg1227122954 (J) | chr12 | 27122954 | T | C | 54.70% | 0.63% | T -> C |
LOC_Os12g43660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g43660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.147; most accessible tissue: Minghui63 panicle, score: 90.624 |
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