71 variations found. LOC_Os01g02460 (receptor kinase LRK10; putative; expressed), ranging from 794,498 bp to 795,413 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100794499 (J) | chr01 | 794499 | A | G | 50.00% | 17.99% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.422; most accessible tissue: Callus, score: 52.610 |
| vg0100794507 (J) | chr01 | 794507 | A | T | 49.30% | 18.07% | A -> T | NA |
LOC_Os01g02460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 33.334; most accessible tissue: Callus, score: 52.610 |
| vg0100794508 (J) | chr01 | 794508 | G | A | 67.30% | 14.45% | G -> A |
LOC_Os01g02460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.156; most accessible tissue: Callus, score: 52.610 |
|
| vg0100794510 (J) | chr01 | 794510 | A | G | 49.00% | 18.26% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.156; most accessible tissue: Callus, score: 52.610 |
| vg0100794525 (J) | chr01 | 794525 | G | A | 59.80% | 11.68% | G -> A | NA |
LOC_Os01g02460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 35.195; most accessible tissue: Callus, score: 52.610 |
| vg0100794540 (J) | chr01 | 794540 | T | C | 70.90% | 11.36% | T -> C | NA |
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 35.944; most accessible tissue: Minghui63 flag leaf, score: 54.348 |
| vg0100794541 (J) | chr01 | 794541 | G | A | 86.40% | 9.39% | G -> A | NA |
LOC_Os01g02460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 35.944; most accessible tissue: Minghui63 flag leaf, score: 54.348 |
| vg0100794546 (J) | chr01 | 794546 | G | A | 61.90% | 12.80% | G -> A | NA |
LOC_Os01g02460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 36.195; most accessible tissue: Minghui63 flag leaf, score: 55.781 |
| vg0100794571 (J) | chr01 | 794571 | C | T | 56.10% | 18.75% | C -> T | NA |
LOC_Os01g02460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.975; most accessible tissue: Callus, score: 52.610 |
| vg0100794637 (J) | chr01 | 794637 | T | C | 55.80% | 18.71% | T -> C |
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 41.033; most accessible tissue: Minghui63 flag leaf, score: 63.086 |
|
| vg0100794676 (J) | chr01 | 794676 | G | A | 56.60% | 22.70% | G -> A | NA |
LOC_Os01g02460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 48.374; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0100794688 (J) | chr01 | 794688 | C | T | 90.10% | 9.04% | C -> T | NA |
LOC_Os01g02460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 48.595; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0100794694 (J) | chr01 | 794694 | C | A | 66.90% | 9.78% | C -> A |
LOC_Os01g02460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 48.788; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
|
| vg0100794699 (J) | chr01 | 794699 | A | C | 55.60% | 10.62% | A -> C |
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 48.957; most accessible tissue: Minghui63 flag leaf, score: 68.675 |
|
| vg0100794718 (J) | chr01 | 794718 | C | A | 71.80% | 11.83% | C -> A | NA |
LOC_Os01g02460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.727; most accessible tissue: Minghui63 flag leaf, score: 68.675 |
| vg0100794722 (J) | chr01 | 794722 | A | G | 72.80% | 15.79% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.632; most accessible tissue: Minghui63 flag leaf, score: 67.635 |
| vg0100794724 (J) | chr01 | 794724 | A | G | 72.40% | 16.21% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.632; most accessible tissue: Minghui63 flag leaf, score: 67.635 |
| vg0100794732 (J) | chr01 | 794732 | C | T | 72.00% | 16.46% | C -> T | NA |
LOC_Os01g02460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.178; most accessible tissue: Minghui63 flag leaf, score: 69.681 |
| vg0100794735 (J) | chr01 | 794735 | T | C | 84.10% | 10.26% | T -> C | NA |
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 50.089; most accessible tissue: Minghui63 flag leaf, score: 69.182 |
| vg0100794753 (J) | chr01 | 794753 | A | G | 64.20% | 15.72% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.901; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0100794764 (J) | chr01 | 794764 | A | AGC | 86.30% | 10.05% | A -> AGC | NA |
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: AGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 49.827; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0100794765 (J) | chr01 | 794765 | A | G | 56.70% | 22.92% | A -> G | NA |
LOC_Os01g02460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.921; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0100794766 (J) | chr01 | 794766 | TAC | T | 85.50% | 10.50% | TAC -> T | NA |
LOC_Os01g02460.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.490; most accessible tissue: Minghui63 flag leaf, score: 69.681 |
| vg0100794768 (J) | chr01 | 794768 | C | T | 62.10% | 21.58% | C -> T | NA |
LOC_Os01g02460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.490; most accessible tissue: Minghui63 flag leaf, score: 69.681 |
| vg0100794777 (J) | chr01 | 794777 | T | G | 48.30% | 13.48% | T -> G |
mr1060_2 (All); LR P-value: 2.64E-07;
mr1060_2 (Ind_All); LR P-value: 2.72E-06; mr1175_2 (Ind_All); LR P-value: 6.29E-06; mr1296_2 (All); LR P-value: 4.45E-06; mr1568_2 (Ind_All); LR P-value: 4.36E-06; mr1576_2 (All); LR P-value: 4.26E-09; mr1882_2 (All); LR P-value: 3.91E-06; mr1882_2 (Ind_All); LR P-value: 3.49E-06 |
LOC_Os01g02460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g02460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.325; most accessible tissue: Minghui63 flag leaf, score: 70.648 |
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