58 variations found. LOC_Os01g43760 (cytochrome P450 72A1; putative; expressed), ranging from 25,070,715 bp to 25,072,705 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0125072060 (J) | chr01 | 25072060 | TGC | TGT | 97.00% | 0.00% | TGC -> TGT | NA |
|
| STR0125072353 (J) | chr01 | 25072353 | AGATTGA GATC | AGATTGA GATT | 66.40% | 0.00% | AGATTGAGAT T -> AGATTGAGAT C | NA |
|
| vg0125070814 (J) | chr01 | 25070814 | G | C | 96.90% | 0.00% | G -> C | NA |
LOC_Os01g43760.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.040; most accessible tissue: Callus, score: 98.170 |
| vg0125070832 (J) | chr01 | 25070832 | G | T | 91.60% | 0.00% | G -> T | NA |
LOC_Os01g43760.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.599; most accessible tissue: Minghui63 flag leaf, score: 95.321 |
| vg0125070837 (J) | chr01 | 25070837 | T | G | 60.10% | 0.00% | G -> T,A | NA |
LOC_Os01g43760.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g43760.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os01g43774.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g43750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.516; most accessible tissue: Minghui63 flag leaf, score: 95.215 |
| vg0125070931 (J) | chr01 | 25070931 | A | G | 69.20% | 0.00% | G -> A |
mr1027 (All); LR P-value: 6.33E-71;
mr1133 (All); LR P-value: 2.05E-18; mr1188 (All); LMM P-value: 1.30E-06; LR P-value: 1.73E-12; mr1188 (Jap_All); LR P-value: 8.46E-08; mr1392 (All); LR P-value: 1.27E-06; mr1414 (All); LR P-value: 1.28E-27; mr1698 (All); LR P-value: 1.18E-21; mr1845 (All); LR P-value: 3.38E-19; mr1924 (All); LR P-value: 5.41E-13; mr1027_2 (All); LR P-value: 1.35E-80; mr1133_2 (All); LR P-value: 1.06E-14; mr1188_2 (Jap_All); LR P-value: 5.51E-07; mr1238_2 (All); LR P-value: 1.99E-28; mr1448_2 (All); LR P-value: 1.22E-34; mr1484_2 (All); LR P-value: 4.43E-25; mr1841_2 (All); LR P-value: 1.65E-32 |
LOC_Os01g43760.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.939; most accessible tissue: Minghui63 flag leaf, score: 95.107 |
| vg0125071024 (J) | chr01 | 25071024 | C | T | 69.40% | 0.00% | T -> C |
mr1027 (All); LR P-value: 5.32E-70;
mr1133 (All); LR P-value: 5.08E-18; mr1188 (All); LR P-value: 4.28E-11; mr1188 (Jap_All); LR P-value: 2.36E-06; mr1392 (All); LR P-value: 2.25E-06; mr1414 (All); LR P-value: 9.95E-28; mr1563 (All); LR P-value: 4.10E-44; mr1845 (All); LR P-value: 2.20E-19; mr1238_2 (All); LR P-value: 4.66E-28; mr1448_2 (All); LR P-value: 6.37E-34; mr1484_2 (All); LR P-value: 1.07E-24; mr1841_2 (All); LR P-value: 9.14E-32 |
LOC_Os01g43760.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.587; most accessible tissue: Zhenshan97 flag leaf, score: 93.925 |
| vg0125071187 (J) | chr01 | 25071187 | G | C | 99.30% | 0.00% | G -> C | NA |
LOC_Os01g43760.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g43774.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g43750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.775; most accessible tissue: Callus, score: 94.817 |
| vg0125071303 (J) | chr01 | 25071303 | G | GCTTTTT | 89.00% | 1.52% | G -> GCTTTTT,GC CTTTTCTTCT TCTTCTTCTT CTT,GCTTTT TCTT,GCCTT TTCTTCTTCT TCTTCTT,GC TTTTTCTTCT T | NA |
LOC_Os01g43774.1 Alt: GCTTTTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: GCTTTTTCTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: GCTTTTTCTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: GCTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: GCTTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: GCTTTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: GCCTTTTCTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: GCCTTTTCTTCTTCTTCTTCTTCTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: GCCTTTTCTTCTTCTTCTTCTTCTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: GCCTTTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: GCCTTTTCTTCTTCTTCTTCTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: GCCTTTTCTTCTTCTTCTTCTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: GCTTTTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: GCTTTTTCTTCTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: GCTTTTTCTTCTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.099; most accessible tissue: Callus, score: 94.817 |
| vg0125071304 (J) | chr01 | 25071304 | C | CTTT | 95.10% | 0.25% | C -> CTTT,CCTT | NA |
LOC_Os01g43774.1 Alt: CCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: CCTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: CCTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.099; most accessible tissue: Callus, score: 94.817 |
| vg0125071305 (J) | chr01 | 25071305 | T | C | 63.90% | 23.72% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g43774.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.099; most accessible tissue: Callus, score: 94.817 |
| vg0125071307 (J) | chr01 | 25071307 | C | T | 43.80% | 26.98% | C -> T | NA |
LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.078; most accessible tissue: Callus, score: 94.817 |
| vg0125071308 (J) | chr01 | 25071308 | TTCTCTC TCTCTC | T | 95.00% | 0.13% | TTCTCTCTCT CTC -> T,TTCTCTCT CTCTCTCTCT CTCTC,TTCT C,TTCTCTCT CTCTCTCTCT CTC,TTCTCT C,TTCTCTCT CTCTCTCTC | NA |
LOC_Os01g43774.1 Alt: TTCTCTCTCTCTCTCTCTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: TTCTCTCTCTCTCTCTCTCTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: TTCTCTCTCTCTCTCTCTCTCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: TTCTCTCTCTCTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: TTCTCTCTCTCTCTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: TTCTCTCTCTCTCTCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: TTCTCTCTCTCTCTCTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: TTCTCTCTCTCTCTCTCTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: TTCTCTCTCTCTCTCTCTCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: TTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: TTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: TTCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: TTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: TTCTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: TTCTCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.078; most accessible tissue: Callus, score: 94.817 |
| vg0125071310 (J) | chr01 | 25071310 | C | CTTCTTC TTCTTCT TCTTCTT CT | 94.80% | 2.45% | C -> CTTCTTCTTC TTCTTCTTCT TCT | NA |
LOC_Os01g43774.1 Alt: CTTCTTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: CTTCTTCTTCTTCTTCTTCTTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: CTTCTTCTTCTTCTTCTTCTTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.054; most accessible tissue: Callus, score: 94.817 |
| vg0125071311 (J) | chr01 | 25071311 | TC | T | 84.00% | 3.72% | TC -> T | NA |
LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.055; most accessible tissue: Callus, score: 94.817 |
| vg0125071314 (J) | chr01 | 25071314 | C | CTTCT | 47.20% | 33.54% | C -> CTTCT,T | NA |
LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g43774.1 Alt: CTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: CTTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: CTTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.049; most accessible tissue: Callus, score: 94.817 |
| vg0125071315 (J) | chr01 | 25071315 | TC | T | 93.60% | 0.83% | TC -> T | NA |
LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.049; most accessible tissue: Callus, score: 94.817 |
| vg0125071319 (J) | chr01 | 25071319 | TC | T | 90.60% | 5.88% | TC -> T | NA |
LOC_Os01g43774.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.153; most accessible tissue: Callus, score: 94.817 |
| vg0125071322 (J) | chr01 | 25071322 | C | CT | 95.70% | 3.70% | C -> CT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g43774.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43750.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43760.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.184; most accessible tissue: Callus, score: 94.817 |
| vg0125071402 (J) | chr01 | 25071402 | CAT | C | 60.30% | 0.00% | C -> CAT | NA |
LOC_Os01g43760.1 Alt: CAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 75.847; most accessible tissue: Minghui63 flag leaf, score: 90.593 |
| vg0125071420 (J) | chr01 | 25071420 | T | C | 69.60% | 0.00% | C -> T |
mr1027 (All); LR P-value: 1.71E-66;
mr1133 (All); LR P-value: 1.67E-18; mr1188 (All); LR P-value: 4.58E-11; mr1188 (Jap_All); LR P-value: 5.99E-06; mr1392 (All); LR P-value: 1.76E-06; mr1414 (All); LR P-value: 1.94E-27; mr1563 (All); LR P-value: 8.92E-44; mr1698 (All); LR P-value: 1.43E-21; mr1845 (All); LR P-value: 2.88E-19; mr1448_2 (All); LR P-value: 1.07E-34 |
LOC_Os01g43760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.159; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
| vg0125071474 (J) | chr01 | 25071474 | CTCGT | C | 62.60% | 2.60% | CTCGT -> C | NA |
LOC_Os01g43760.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g43760.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 69.349; most accessible tissue: Callus, score: 91.446 |
| vg0125071479 (J) | chr01 | 25071479 | AC | A | 62.60% | 2.58% | AC -> A | NA |
LOC_Os01g43760.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g43760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 68.928; most accessible tissue: Callus, score: 91.446 |
| vg0125071482 (J) | chr01 | 25071482 | AGGTGGA T | A | 63.20% | 2.58% | AGGTGGAT -> A | NA |
LOC_Os01g43760.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g43760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 68.231; most accessible tissue: Callus, score: 91.446 |
| vg0125071491 (J) | chr01 | 25071491 | T | C | 62.60% | 2.60% | T -> C | NA |
LOC_Os01g43760.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g43760.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 67.897; most accessible tissue: Callus, score: 91.446 |
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