20 variations found. LOC_Os01g14180 (expressed protein), ranging from 7,945,213 bp to 7,946,972 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0107945288 (J) | chr01 | 7945288 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g14170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g14190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14180.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.568; most accessible tissue: Callus, score: 69.101 |
| vg0107945328 (J) | chr01 | 7945328 | G | T | 90.90% | 0.76% | G -> T |
mr1098 (All); LR P-value: 1.57E-28;
mr1099 (All); LR P-value: 5.99E-27; mr1113 (All); LR P-value: 2.20E-17; mr1114 (All); LR P-value: 2.77E-18; mr1120 (All); LR P-value: 6.79E-22; mr1166 (All); LR P-value: 2.04E-13; mr1247 (All); LR P-value: 3.20E-22; mr1286 (All); LR P-value: 3.88E-07; mr1409 (All); LR P-value: 1.65E-11; mr1420 (All); LR P-value: 1.85E-06; mr1465 (All); LR P-value: 4.06E-09; mr1515 (All); LR P-value: 2.57E-18; mr1589 (All); LR P-value: 6.45E-22; mr1777 (All); LR P-value: 6.59E-06; mr1868 (All); LR P-value: 7.75E-25; mr1961 (All); LR P-value: 2.87E-19; mr1120_2 (All); LR P-value: 9.11E-22; mr1240_2 (All); LR P-value: 2.57E-17; mr1247_2 (All); LR P-value: 2.03E-22; mr1388_2 (All); LR P-value: 3.69E-10; mr1510_2 (All); LR P-value: 1.09E-07; mr1583_2 (All); LR P-value: 7.38E-14; mr1740_2 (All); LR P-value: 1.20E-06; mr1741_2 (All); LR P-value: 5.88E-09; mr1961_2 (All); LR P-value: 5.64E-15 |
LOC_Os01g14170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g14190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14180.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 44.166; most accessible tissue: Zhenshan97 young leaf, score: 65.804 |
| vg0107945333 (J) | chr01 | 7945333 | CTG | CTGTG | 90.70% | 0.00% | CTG -> CTGTG,C | NA |
LOC_Os01g14170.1 Alt: CTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g14190.1 Alt: CTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14180.1 Alt: CTGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14170.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14190.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14180.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.130; most accessible tissue: Zhenshan97 young leaf, score: 63.096 |
| vg0107945736 (J) | chr01 | 7945736 | A | G | 92.50% | 0.00% | A -> G |
mr1113 (All); LR P-value: 1.36E-15;
mr1120 (All); LR P-value: 5.76E-21; mr1166 (All); LR P-value: 1.87E-13; mr1286 (All); LR P-value: 4.83E-07; mr1320 (All); LR P-value: 2.65E-06; mr1409 (All); LR P-value: 1.36E-12; mr1465 (All); LR P-value: 4.53E-09; mr1515 (All); LR P-value: 7.77E-19; mr1649 (All); LR P-value: 4.64E-12; mr1777 (All); LR P-value: 7.78E-06; mr1388_2 (All); LR P-value: 3.51E-10; mr1530_2 (All); LR P-value: 8.47E-15; mr1740_2 (All); LR P-value: 1.05E-06; mr1741_2 (All); LR P-value: 3.41E-09 |
LOC_Os01g14180.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.207; most accessible tissue: Zhenshan97 young leaf, score: 83.199 |
| vg0107945888 (J) | chr01 | 7945888 | G | T | 99.50% | 0.00% | G -> T | NA |
LOC_Os01g14180.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.207; most accessible tissue: Zhenshan97 young leaf, score: 95.473 |
| vg0107945949 (J) | chr01 | 7945949 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.149; most accessible tissue: Zhenshan97 young leaf, score: 96.015 |
| vg0107946037 (J) | chr01 | 7946037 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.810; most accessible tissue: Zhenshan97 young leaf, score: 96.823 |
| vg0107946042 (J) | chr01 | 7946042 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os01g14180.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.816; most accessible tissue: Zhenshan97 young leaf, score: 96.857 |
| vg0107946090 (J) | chr01 | 7946090 | G | T | 55.30% | 30.60% | G -> T | NA |
LOC_Os01g14180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g14180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.022; most accessible tissue: Zhenshan97 young leaf, score: 96.974 |
| vg0107946118 (J) | chr01 | 7946118 | C | T | 55.00% | 31.27% | C -> T | NA |
LOC_Os01g14180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g14180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.096; most accessible tissue: Zhenshan97 young leaf, score: 97.132 |
| vg0107946121 (J) | chr01 | 7946121 | G | A | 55.00% | 31.29% | G -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g14180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.079; most accessible tissue: Zhenshan97 young leaf, score: 97.132 |
| vg0107946179 (J) | chr01 | 7946179 | G | A | 60.50% | 28.21% | G -> A | NA |
LOC_Os01g14180.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g14180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.307; most accessible tissue: Zhenshan97 young leaf, score: 96.811 |
| vg0107946191 (J) | chr01 | 7946191 | G | Unkown | 60.40% | 28.27% | G -> C | NA |
LOC_Os01g14180.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os01g14170.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.236; most accessible tissue: Zhenshan97 young leaf, score: 96.550 |
| vg0107946192 (J) | chr01 | 7946192 | G | Unkown | 60.40% | 28.21% | G -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.229; most accessible tissue: Zhenshan97 young leaf, score: 96.550 |
| vg0107946196 (J) | chr01 | 7946196 | C | Unkown | 60.50% | 28.18% | C -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.316; most accessible tissue: Zhenshan97 young leaf, score: 96.588 |
| vg0107946214 (J) | chr01 | 7946214 | G | A | 61.50% | 26.28% | G -> A | NA |
LOC_Os01g14180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g14180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.447; most accessible tissue: Zhenshan97 young leaf, score: 96.563 |
| vg0107946281 (J) | chr01 | 7946281 | C | T | 98.90% | 0.42% | C -> T | NA |
LOC_Os01g14180.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g14170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.053; most accessible tissue: Zhenshan97 young leaf, score: 95.007 |
| vg0107946286 (J) | chr01 | 7946286 | C | T | 99.60% | 0.17% | C -> T | NA |
LOC_Os01g14180.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g14170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.035; most accessible tissue: Zhenshan97 young leaf, score: 94.955 |
| vg0107946331 (J) | chr01 | 7946331 | G | T | 92.10% | 0.00% | G -> T |
mr1095 (All); LR P-value: 8.84E-22;
mr1098 (All); LR P-value: 7.22E-30; mr1099 (All); LR P-value: 3.05E-27; mr1101 (All); LR P-value: 5.76E-26; mr1113 (All); LR P-value: 5.66E-19; mr1114 (All); LR P-value: 1.45E-19; mr1117 (All); LR P-value: 4.47E-20; mr1119 (All); LR P-value: 1.28E-17; mr1120 (All); LR P-value: 1.42E-23; mr1123 (All); LR P-value: 2.42E-23; mr1166 (All); LR P-value: 1.23E-14; mr1210 (All); LR P-value: 1.25E-21; mr1247 (All); LR P-value: 1.84E-23; mr1286 (All); LR P-value: 4.32E-07; mr1305 (All); LR P-value: 1.54E-23; mr1409 (All); LR P-value: 2.37E-12; mr1465 (All); LR P-value: 7.19E-09; mr1496 (All); LR P-value: 3.76E-14; mr1515 (All); LR P-value: 6.79E-19; mr1549 (All); LR P-value: 1.67E-38; mr1589 (All); LR P-value: 1.06E-22; mr1649 (All); LR P-value: 1.14E-11; mr1777 (All); LR P-value: 4.51E-06; mr1868 (All); LR P-value: 8.16E-27; mr1918 (All); LR P-value: 1.19E-12; mr1936 (All); LR P-value: 2.17E-18; mr1961 (All); LR P-value: 3.51E-20; mr1098_2 (All); LR P-value: 7.29E-30; mr1099_2 (All); LR P-value: 1.75E-23; mr1113_2 (All); LR P-value: 5.43E-18; mr1114_2 (All); LR P-value: 1.50E-17; mr1117_2 (All); LR P-value: 6.32E-20; mr1119_2 (All); LR P-value: 1.37E-17; mr1120_2 (All); LR P-value: 3.55E-24; mr1240_2 (All); LR P-value: 2.37E-19; mr1247_2 (All); LR P-value: 3.21E-24; mr1388_2 (All); LR P-value: 3.32E-11; mr1530_2 (All); LR P-value: 3.29E-15; mr1583_2 (All); LR P-value: 1.57E-14; mr1740_2 (All); LR P-value: 1.83E-06; mr1817_2 (All); LR P-value: 3.75E-18; mr1911_2 (All); LR P-value: 2.41E-14; mr1961_2 (All); LR P-value: 2.03E-16 |
LOC_Os01g14180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.782; most accessible tissue: Zhenshan97 young leaf, score: 94.425 |
| vg0107946790 (J) | chr01 | 7946790 | CGGA | C | 99.20% | 0.00% | CGGA -> C | NA |
LOC_Os01g14180.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 78.790; most accessible tissue: Zhenshan97 panicle, score: 91.693 |