14 variations found. LOC_Os01g43440 (TOO MANY MOUTHS precursor; putative; expressed), ranging from 24,855,936 bp to 24,857,421 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 |
---|---|---|---|---|---|---|---|---|---|
vg0124856043 (J) | chr01 | 24856043 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g43430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g43450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.209; most accessible tissue: Callus, score: 97.399 |
vg0124856227 (J) | chr01 | 24856227 | C | G | 73.80% | 0.00% | G -> C |
mr1005 (All); LR P-value: 1.64E-09;
mr1133 (All); LR P-value: 1.99E-17; mr1622 (All); LR P-value: 8.72E-07; mr1830 (All); LR P-value: 1.99E-16; mr1924 (All); LR P-value: 5.87E-13; mr1019_2 (All); LR P-value: 3.32E-69; mr1679_2 (All); LR P-value: 1.04E-20; mr1771_2 (All); LR P-value: 6.16E-39; mr1784_2 (All); LR P-value: 5.76E-45 |
LOC_Os01g43440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.729; most accessible tissue: Zhenshan97 panicle, score: 95.654 |
vg0124856633 (J) | chr01 | 24856633 | G | T | 68.30% | 0.57% | G -> T | NA |
LOC_Os01g43440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.784; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
vg0124856754 (J) | chr01 | 24856754 | G | A | 95.50% | 0.00% | G -> A | NA |
LOC_Os01g43440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 88.393; most accessible tissue: Zhenshan97 panicle, score: 93.657 |
vg0124856854 (J) | chr01 | 24856854 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 87.834; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
vg0124857038 (J) | chr01 | 24857038 | C | T | 93.60% | 0.00% | C -> T | NA |
LOC_Os01g43440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.202; most accessible tissue: Zhenshan97 panicle, score: 95.016 |
vg0124857248 (J) | chr01 | 24857248 | G | A | 73.70% | 0.00% | A -> G |
mr1005 (All); LR P-value: 4.27E-09;
mr1188 (All); LR P-value: 1.40E-10; mr1575 (All); LR P-value: 3.16E-09; mr1622 (All); LR P-value: 4.72E-07; mr1830 (All); LR P-value: 8.24E-17; mr1924 (All); LR P-value: 2.91E-13; mr1679_2 (All); LR P-value: 3.63E-22; mr1771_2 (All); LR P-value: 1.10E-39; mr1784_2 (All); LR P-value: 5.60E-45 |
LOC_Os01g43440.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.648; most accessible tissue: Minghui63 panicle, score: 95.915 |
vg0124857349 (J) | chr01 | 24857349 | C | T | 95.50% | 0.00% | C -> T | NA |
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.588; most accessible tissue: Minghui63 panicle, score: 96.161 |
vg0124857369 (J) | chr01 | 24857369 | ACGG | A | 99.40% | 0.00% | ACGG -> A | NA |
LOC_Os01g43440.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os01g43450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g43460.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g43460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.673; most accessible tissue: Minghui63 panicle, score: 96.113 |
vg0124857371 (J) | chr01 | 24857371 | G | C | 68.90% | 0.40% | G -> C |
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g43440.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 89.776; most accessible tissue: Minghui63 panicle, score: 96.113 |
|
vg0124857372 (J) | chr01 | 24857372 | G | A | 68.90% | 0.40% | G -> A | NA |
LOC_Os01g43440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.771; most accessible tissue: Minghui63 panicle, score: 96.113 |
vg0124857381 (J) | chr01 | 24857381 | A | G | 43.20% | 0.47% | A -> G,ACCG | NA |
LOC_Os01g43440.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: ACCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.735; most accessible tissue: Minghui63 panicle, score: 96.207 |
vg0124857385 (J) | chr01 | 24857385 | C | T | 73.70% | 0.00% | T -> C |
LOC_Os01g43440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.718; most accessible tissue: Minghui63 panicle, score: 96.207 |
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STR0124857386 (J) | chr01 | 24857386 | CGCCGCC GCCG | CGCCGCC GCCGCCG | 67.60% | 0.00% | CGCCGCCGCC G -> CGCCGCCGCC GCCG | NA |
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