19 variations found. LOC_Os08g12500 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 7,396,802 bp to 7,404,724 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0807397196 (J) | chr08 | 7397196 | C | T | 32.60% | 64.79% | C -> T | NA |
LOC_Os08g12500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.507; most accessible tissue: Minghui63 young leaf, score: 14.915 |
| vg0807397545 (J) | chr08 | 7397545 | T | C | 0.20% | 97.82% | C -> T | NA |
LOC_Os08g12500.1 Alt: T/stop_gained(CooVar)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0807397578 (J) | chr08 | 7397578 | A | G | 0.20% | 97.76% | G -> A | NA |
LOC_Os08g12500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0807399608 (J) | chr08 | 7399608 | A | G | 33.00% | 63.50% | A -> G | NA |
LOC_Os08g12500.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.605; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399710 (J) | chr08 | 7399710 | GT | G | 35.10% | 61.64% | GT -> G | NA |
LOC_Os08g12500.1 Alt: G/frameshift_variant(CooVar)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.692; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399714 (J) | chr08 | 7399714 | C | T | 35.10% | 61.62% | C -> T | NA |
LOC_Os08g12500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.692; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399716 (J) | chr08 | 7399716 | C | A | 35.10% | 61.38% | C -> A | NA |
LOC_Os08g12500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.692; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399752 (J) | chr08 | 7399752 | G | A | 35.20% | 60.18% | G -> A | NA |
LOC_Os08g12500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.692; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399839 (J) | chr08 | 7399839 | G | A | 30.90% | 60.94% | G -> A |
mr1114 (Jap_All); LR P-value: 2.68E-06;
mr1117 (Jap_All); LR P-value: 5.84E-07; mr1118 (Jap_All); LR P-value: 7.71E-07; mr1119 (Jap_All); LR P-value: 4.81E-07; mr1123 (Jap_All); LR P-value: 4.98E-06; mr1180 (Jap_All); LR P-value: 8.29E-08; mr1183 (Jap_All); LR P-value: 2.02E-06; mr1242 (Jap_All); LR P-value: 6.39E-06; mr1496 (Jap_All); LR P-value: 4.26E-07; mr1503 (Jap_All); LR P-value: 4.29E-06; mr1961 (Jap_All); LR P-value: 5.59E-06; mr1063_2 (Jap_All); LR P-value: 1.09E-06; mr1177_2 (Jap_All); LR P-value: 1.63E-06; mr1180_2 (Jap_All); LR P-value: 1.50E-10; mr1183_2 (Jap_All); LR P-value: 3.26E-11; mr1240_2 (Jap_All); LR P-value: 7.86E-06; mr1289_2 (Jap_All); LR P-value: 9.42E-06; mr1496_2 (Jap_All); LR P-value: 5.25E-07; mr1764_2 (Jap_All); LR P-value: 6.50E-06; mr1794_2 (Jap_All); LR P-value: 1.46E-09 |
LOC_Os08g12500.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.692; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0807399852 (J) | chr08 | 7399852 | CAT | CATAT | 25.10% | 63.61% | CATAT -> CAT,C,CATA TAT,CATATA TAT | NA |
LOC_Os08g12500.1 Alt: CATATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g12500.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g12500.1 Alt: CAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g12500.1 Alt: CATATATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.499; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0807399977 (J) | chr08 | 7399977 | G | C | 33.10% | 62.74% | G -> C | NA |
LOC_Os08g12500.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.412; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0807399979 (J) | chr08 | 7399979 | A | T | 33.00% | 63.84% | A -> T | NA |
LOC_Os08g12500.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.412; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0807400007 (J) | chr08 | 7400007 | G | A | 33.70% | 61.47% | G -> A | NA |
LOC_Os08g12500.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.393; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0807400176 (J) | chr08 | 7400176 | A | T | 35.50% | 60.43% | A -> T | NA |
LOC_Os08g12500.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.449; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0807400180 (J) | chr08 | 7400180 | A | G | 35.80% | 60.39% | A -> G | NA |
LOC_Os08g12500.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.449; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0807401375 (J) | chr08 | 7401375 | G | A | 39.30% | 58.55% | G -> A | NA |
LOC_Os08g12500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.318; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0807401447 (J) | chr08 | 7401447 | G | C | 39.40% | 54.21% | G -> C | NA |
LOC_Os08g12500.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.184; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0807401951 (J) | chr08 | 7401951 | C | T | 22.70% | 63.54% | C -> T | NA |
LOC_Os08g12500.1 Alt: T/stop_gained(CooVar)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.271; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 |
| vg0807402433 (J) | chr08 | 7402433 | G | A | 34.70% | 58.15% | G -> A | NA |
LOC_Os08g12500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g12500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.255; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 |