110 variations found. Os01g0872400/LOC_Os01g65190 (POT domain containing peptide transporter; putative; expressed), ranging from 37,828,273 bp to 37,832,381 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g65190 | POT domain containing peptide transporter, putative, expressed; RAP ID: Os01g0872400; MSU ID: LOC_Os01g65190 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137828395 (J) | chr01 | 37828395 | G | C | 77.40% | 0.00% | G -> C |
mr1375 (Ind_All); LR P-value: 7.25E-07;
mr1517 (All); LMM P-value: 1.02E-08; mr1517 (Ind_All); LMM P-value: 3.43E-14; LR P-value: 2.47E-16; mr1538 (All); LMM P-value: 3.13E-08; mr1538 (Ind_All); LMM P-value: 3.96E-11; LR P-value: 1.81E-13; mr1517_2 (All); LMM P-value: 1.65E-09; mr1517_2 (Ind_All); LMM P-value: 4.91E-16; LR P-value: 2.12E-16; mr1538_2 (All); LMM P-value: 8.54E-08; mr1538_2 (Ind_All); LMM P-value: 5.05E-12; LR P-value: 3.13E-17 |
LOC_Os01g65190.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65169.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.482; most accessible tissue: Zhenshan97 flower, score: 96.097 |
| vg0137828701 (J) | chr01 | 37828701 | C | A | 64.80% | 0.00% | A -> C | NA |
LOC_Os01g65190.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.360; most accessible tissue: Zhenshan97 flower, score: 97.169 |
| vg0137828706 (J) | chr01 | 37828706 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os01g65190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.412; most accessible tissue: Zhenshan97 flower, score: 97.194 |
| vg0137828754 (J) | chr01 | 37828754 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os01g65190.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g65169.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.958; most accessible tissue: Zhenshan97 flower, score: 97.646 |
| vg0137828777 (J) | chr01 | 37828777 | C | T | 64.80% | 0.00% | T -> C | NA |
LOC_Os01g65190.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.285; most accessible tissue: Zhenshan97 flower, score: 97.660 |
| vg0137828798 (J) | chr01 | 37828798 | C | T | 94.90% | 0.00% | C -> T | NA |
LOC_Os01g65190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.645; most accessible tissue: Zhenshan97 flower, score: 97.789 |
| vg0137828945 (J) | chr01 | 37828945 | C | G | 82.70% | 0.00% | C -> G |
mr1375 (Ind_All); LR P-value: 8.44E-07;
mr1517 (All); LMM P-value: 1.42E-09; mr1517 (Ind_All); LMM P-value: 4.86E-14; LR P-value: 3.50E-16; mr1538 (All); LMM P-value: 5.99E-09; mr1538 (Ind_All); LMM P-value: 5.07E-11; LR P-value: 2.19E-13; mr1517_2 (All); LMM P-value: 3.63E-09; mr1517_2 (Ind_All); LMM P-value: 9.28E-16; LR P-value: 3.84E-16; mr1538_2 (All); LMM P-value: 8.40E-08; mr1538_2 (Ind_All); LMM P-value: 9.61E-12; LR P-value: 6.25E-17 |
LOC_Os01g65169.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.998; most accessible tissue: Zhenshan97 flower, score: 97.082 |
| vg0137829039 (J) | chr01 | 37829039 | T | C | 64.80% | 0.00% | C -> T | NA |
LOC_Os01g65169.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.592; most accessible tissue: Zhenshan97 flower, score: 96.885 |
| vg0137829042 (J) | chr01 | 37829042 | C | T | 94.70% | 0.00% | C -> T | NA |
LOC_Os01g65169.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.505; most accessible tissue: Zhenshan97 flower, score: 96.855 |
| vg0137829106 (J) | chr01 | 37829106 | G | A | 58.20% | 0.00% | G -> A |
mr1170 (All); LR P-value: 1.01E-12;
mr1375 (All); LMM P-value: 9.10E-09; LR P-value: 5.25E-26; mr1375 (Ind_All); LMM P-value: 3.82E-06; LR P-value: 3.38E-08; mr1517 (All); LMM P-value: 2.36E-20; mr1517 (Ind_All); LMM P-value: 1.16E-16; LR P-value: 6.58E-20; mr1538 (All); LMM P-value: 6.40E-19; LR P-value: 2.39E-75; mr1538 (Ind_All); LMM P-value: 3.84E-12; LR P-value: 2.05E-14; mr1517_2 (All); LMM P-value: 2.58E-24; mr1517_2 (Ind_All); LMM P-value: 2.98E-18; LR P-value: 3.66E-21; mr1538_2 (All); LMM P-value: 1.34E-19; mr1538_2 (Ind_All); LMM P-value: 1.65E-12; LR P-value: 4.49E-19 |
LOC_Os01g65169.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.399; most accessible tissue: Zhenshan97 flower, score: 95.578 |
| vg0137829128 (J) | chr01 | 37829128 | AT | A | 99.50% | 0.00% | AT -> TT,A | NA |
LOC_Os01g65169.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: TT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: TT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.182; most accessible tissue: Zhenshan97 flower, score: 95.299 |
| vg0137829162 (J) | chr01 | 37829162 | G | C | 97.90% | 0.00% | G -> C | NA |
LOC_Os01g65169.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.729; most accessible tissue: Zhenshan97 flower, score: 93.774 |
| vg0137829172 (J) | chr01 | 37829172 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os01g65169.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65190.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.976; most accessible tissue: Zhenshan97 flower, score: 93.448 |
| vg0137829176 (J) | chr01 | 37829176 | G | A | 77.10% | 0.19% | G -> A |
mr1375 (Ind_All); LR P-value: 5.78E-07;
mr1517 (All); LMM P-value: 4.32E-08; mr1517 (Ind_All); LMM P-value: 3.08E-13; LR P-value: 1.04E-15; mr1538 (All); LMM P-value: 9.11E-08; mr1538 (Ind_All); LMM P-value: 3.50E-10; LR P-value: 2.97E-13; mr1517_2 (All); LMM P-value: 3.79E-09; mr1517_2 (Ind_All); LMM P-value: 1.00E-15; LR P-value: 2.14E-16; mr1538_2 (All); LMM P-value: 1.27E-07; mr1538_2 (Ind_All); LMM P-value: 1.33E-12; LR P-value: 5.13E-18 |
LOC_Os01g65169.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.847; most accessible tissue: Zhenshan97 flower, score: 93.405 |
| vg0137829191 (J) | chr01 | 37829191 | A | G | 77.10% | 0.15% | A -> G |
mr1375 (Ind_All); LR P-value: 1.24E-06;
mr1517 (All); LMM P-value: 8.94E-08; mr1517 (Ind_All); LMM P-value: 1.42E-12; LR P-value: 5.99E-15; mr1538 (All); LMM P-value: 9.83E-08; mr1538 (Ind_All); LMM P-value: 4.35E-10; LR P-value: 1.69E-12; mr1517_2 (All); LMM P-value: 3.01E-09; mr1517_2 (Ind_All); LMM P-value: 9.53E-16; LR P-value: 2.06E-16; mr1538_2 (All); LMM P-value: 3.01E-07; mr1538_2 (Ind_All); LMM P-value: 1.05E-11; LR P-value: 8.96E-17 |
LOC_Os01g65200.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 68.276; most accessible tissue: Zhenshan97 flower, score: 92.566 |
| vg0137829266 (J) | chr01 | 37829266 | T | C | 77.10% | 0.08% | T -> C |
mr1375 (Ind_All); LR P-value: 4.78E-07;
mr1517 (All); LMM P-value: 2.42E-08; mr1517 (Ind_All); LMM P-value: 2.54E-13; LR P-value: 6.37E-16; mr1538 (All); LMM P-value: 5.98E-08; mr1538 (Ind_All); LMM P-value: 3.22E-10; LR P-value: 4.59E-13; mr1517_2 (All); LMM P-value: 1.03E-09; mr1517_2 (Ind_All); LMM P-value: 4.91E-16; LR P-value: 5.16E-17; mr1538_2 (All); LMM P-value: 3.02E-08; mr1538_2 (Ind_All); LMM P-value: 3.34E-12; LR P-value: 5.63E-18 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.053; most accessible tissue: Zhenshan97 flower, score: 90.843 |
| vg0137829353 (J) | chr01 | 37829353 | C | CT | 77.20% | 0.00% | C -> CT,CTT | NA |
LOC_Os01g65200.3 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.393; most accessible tissue: Zhenshan97 flower, score: 92.081 |
| vg0137829367 (J) | chr01 | 37829367 | CAA | CAAA | 43.10% | 6.98% | CAA -> CAAA,CA,CA AAA,CAAAAA ,C,AAA | NA |
LOC_Os01g65200.3 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: CAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: CAAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CAAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CAAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: AAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.187; most accessible tissue: Zhenshan97 flower, score: 92.192 |
| vg0137829374 (J) | chr01 | 37829374 | A | AG | 58.00% | 0.00% | A -> AG | NA |
LOC_Os01g65200.3 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65169.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: AG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.557; most accessible tissue: Zhenshan97 flower, score: 92.245 |
| vg0137829593 (J) | chr01 | 37829593 | T | A | 58.30% | 0.06% | T -> A |
mr1170 (All); LR P-value: 4.27E-12;
mr1375 (All); LMM P-value: 4.25E-08; LR P-value: 1.01E-24; mr1375 (Ind_All); LMM P-value: 6.13E-06; LR P-value: 6.29E-08; mr1517 (All); LMM P-value: 7.88E-18; mr1517 (Ind_All); LMM P-value: 1.16E-15; LR P-value: 2.29E-19; mr1538 (All); LMM P-value: 2.97E-17; LR P-value: 9.85E-71; mr1538 (Ind_All); LMM P-value: 4.00E-11; LR P-value: 7.75E-14; mr1517_2 (All); LMM P-value: 1.29E-24; mr1517_2 (Ind_All); LMM P-value: 7.97E-21; LR P-value: 5.10E-23; mr1538_2 (All); LMM P-value: 4.22E-19; mr1538_2 (Ind_All); LMM P-value: 1.08E-13; LR P-value: 1.65E-20 |
LOC_Os01g65190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.912; most accessible tissue: Zhenshan97 flower, score: 94.897 |
| vg0137829682 (J) | chr01 | 37829682 | G | A | 77.00% | 0.32% | G -> A |
mr1375 (Ind_All); LMM P-value: 7.56E-06; LR P-value: 1.07E-07;
mr1517 (All); LMM P-value: 6.94E-09; mr1517 (Ind_All); LMM P-value: 2.51E-14; LR P-value: 1.21E-16; mr1538 (All); LMM P-value: 6.14E-08; mr1538 (Ind_All); LMM P-value: 8.77E-11; LR P-value: 3.34E-13; mr1517_2 (All); LMM P-value: 1.70E-10; mr1517_2 (Ind_All); LMM P-value: 9.66E-18; LR P-value: 1.18E-17; mr1538_2 (All); LMM P-value: 3.07E-08; mr1538_2 (Ind_All); LMM P-value: 4.07E-13; LR P-value: 1.31E-18 |
LOC_Os01g65190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.882; most accessible tissue: Zhenshan97 flower, score: 94.841 |
| vg0137829752 (J) | chr01 | 37829752 | T | G | 77.10% | 0.06% | T -> G |
mr1375 (Ind_All); LR P-value: 3.22E-07;
mr1517 (All); LMM P-value: 8.64E-09; mr1517 (Ind_All); LMM P-value: 7.56E-14; LR P-value: 3.74E-16; mr1538 (All); LMM P-value: 1.68E-08; mr1538 (Ind_All); LMM P-value: 1.25E-10; LR P-value: 5.32E-13; mr1517_2 (All); LMM P-value: 1.79E-10; mr1517_2 (Ind_All); LMM P-value: 4.04E-17; LR P-value: 2.68E-17; mr1538_2 (All); LMM P-value: 7.24E-08; mr1538_2 (Ind_All); LMM P-value: 2.14E-12; LR P-value: 9.42E-18 |
LOC_Os01g65190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.724; most accessible tissue: Zhenshan97 flower, score: 95.050 |
| vg0137829843 (J) | chr01 | 37829843 | C | G | 82.40% | 0.23% | C -> G |
mr1375 (Ind_All); LR P-value: 5.70E-07;
mr1517 (All); LMM P-value: 6.03E-09; mr1517 (Ind_All); LMM P-value: 2.68E-13; LR P-value: 1.40E-15; mr1538 (All); LMM P-value: 3.69E-08; mr1538 (Ind_All); LMM P-value: 3.15E-10; LR P-value: 8.30E-13; mr1517_2 (All); LMM P-value: 7.13E-09; mr1517_2 (Ind_All); LMM P-value: 4.96E-16; LR P-value: 3.80E-16; mr1538_2 (All); LMM P-value: 3.84E-07; mr1538_2 (Ind_All); LMM P-value: 1.92E-11; LR P-value: 1.06E-16 |
LOC_Os01g65190.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.791; most accessible tissue: Zhenshan97 flower, score: 94.601 |
| vg0137829887 (J) | chr01 | 37829887 | GCGCGC | G | 77.10% | 0.32% | GCGCGC -> G | NA |
LOC_Os01g65190.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.445; most accessible tissue: Zhenshan97 flower, score: 94.966 |
| vg0137829896 (J) | chr01 | 37829896 | TCGCGCG | T | 77.10% | 0.32% | TCGCGCG -> T | NA |
LOC_Os01g65190.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g65190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.550; most accessible tissue: Zhenshan97 flower, score: 95.117 |
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