22 variations found. Os03g0761300/LOC_Os03g55340 (pentatricopeptide; putative; expressed), ranging from 31,480,147 bp to 31,483,288 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g55340 | pentatricopeptide, putative, expressed; RAP ID: Os03g0761300; MSU ID: LOC_Os03g55340 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0331480187 (J) | chr03 | 31480187 | T | C | 51.50% | 0.02% | T -> C |
mr1050 (All); LR P-value: 1.50E-10;
mr1118 (All); LR P-value: 1.07E-14; mr1272 (All); LR P-value: 5.43E-13; mr1343 (All); LR P-value: 1.56E-07; mr1354 (Ind_All); LR P-value: 2.43E-06; mr1553 (All); LR P-value: 2.36E-11; mr1680 (All); LR P-value: 2.58E-07; mr1699 (Ind_All); LR P-value: 4.27E-09; mr1829 (All); LMM P-value: 1.00E-06; LR P-value: 2.86E-12; mr1829 (Ind_All); LMM P-value: 1.32E-07; LR P-value: 4.19E-17; mr1835 (All); LR P-value: 4.51E-06; mr1842 (All); LR P-value: 1.82E-22; mr1842 (Ind_All); LR P-value: 1.22E-11; mr1902 (All); LR P-value: 2.02E-17; mr1902 (Ind_All); LR P-value: 4.49E-08; mr1979 (All); LR P-value: 1.42E-07; mr1050_2 (All); LR P-value: 7.06E-10; mr1050_2 (Ind_All); LR P-value: 7.02E-06; mr1699_2 (Ind_All); LMM P-value: 7.05E-07; LR P-value: 1.40E-12; mr1829_2 (All); LMM P-value: 8.68E-06; LR P-value: 9.27E-15; mr1829_2 (Ind_All); LMM P-value: 4.52E-07; LR P-value: 3.69E-20; mr1842_2 (All); LR P-value: 4.19E-23; mr1842_2 (Ind_All); LR P-value: 4.11E-14; mr1902_2 (All); LR P-value: 4.70E-23; mr1902_2 (Ind_All); LR P-value: 5.65E-16; mr1933_2 (All); LR P-value: 5.89E-26; mr1933_2 (Ind_All); LR P-value: 9.01E-09 |
LOC_Os03g55340.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.238 |
| vg0331480224 (J) | chr03 | 31480224 | T | C | 51.40% | 0.32% | T -> C |
mr1050 (All); LR P-value: 3.38E-11;
mr1118 (All); LR P-value: 1.22E-14; mr1272 (All); LR P-value: 3.14E-13; mr1343 (All); LR P-value: 1.82E-07; mr1354 (Ind_All); LR P-value: 1.52E-06; mr1553 (All); LR P-value: 4.06E-11; mr1660 (All); LR P-value: 7.21E-08; mr1680 (All); LR P-value: 2.45E-07; mr1699 (Ind_All); LR P-value: 1.96E-08; mr1829 (All); LMM P-value: 1.85E-06; LR P-value: 4.67E-12; mr1829 (Ind_All); LMM P-value: 1.15E-07; LR P-value: 4.02E-17; mr1835 (All); LR P-value: 5.81E-06; mr1842 (All); LR P-value: 3.20E-22; mr1842 (Ind_All); LR P-value: 5.69E-11; mr1902 (All); LR P-value: 2.18E-17; mr1902 (Ind_All); LR P-value: 8.68E-08; mr1979 (All); LR P-value: 6.47E-08; mr1050_2 (All); LR P-value: 3.30E-10; mr1354_2 (Ind_All); LR P-value: 4.60E-06; mr1699_2 (Ind_All); LMM P-value: 2.10E-06; LR P-value: 6.42E-12; mr1829_2 (All); LR P-value: 2.74E-14; mr1829_2 (Ind_All); LMM P-value: 4.33E-07; LR P-value: 6.26E-20; mr1842_2 (All); LR P-value: 1.18E-22; mr1842_2 (Ind_All); LR P-value: 1.16E-13; mr1902_2 (All); LR P-value: 2.03E-22; mr1902_2 (Ind_All); LR P-value: 5.85E-15; mr1933_2 (All); LR P-value: 6.19E-25; mr1933_2 (Ind_All); LR P-value: 4.94E-08 |
LOC_Os03g55340.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 98.115; most accessible tissue: Zhenshan97 flag leaf, score: 99.335 |
| vg0331480345 (J) | chr03 | 31480345 | G | A | 90.80% | 0.00% | G -> A |
mr1338 (All); LR P-value: 1.97E-06;
mr1425 (All); LR P-value: 4.30E-06; mr1539 (All); LR P-value: 2.00E-08; mr1543 (All); LR P-value: 4.12E-06; mr1551 (Jap_All); LR P-value: 9.34E-09; mr1742 (All); LR P-value: 4.01E-06; mr1871 (All); LR P-value: 2.17E-13; mr1879 (Jap_All); LR P-value: 1.28E-13; mr1174_2 (All); LMM P-value: 2.42E-07; mr1174_2 (Jap_All); LR P-value: 2.29E-06; mr1304_2 (Jap_All); LR P-value: 5.65E-09; mr1347_2 (Jap_All); LR P-value: 1.54E-08; mr1364_2 (All); LR P-value: 1.10E-08; mr1364_2 (Jap_All); LR P-value: 6.17E-10; mr1422_2 (Jap_All); LR P-value: 2.16E-06; mr1551_2 (Jap_All); LR P-value: 1.99E-09; mr1552_2 (All); LR P-value: 4.50E-13; mr1606_2 (Jap_All); LR P-value: 1.80E-06; mr1653_2 (Jap_All); LR P-value: 1.03E-07; mr1696_2 (All); LR P-value: 1.02E-08; mr1696_2 (Jap_All); LR P-value: 1.56E-08; mr1707_2 (Jap_All); LR P-value: 1.50E-06; mr1742_2 (All); LR P-value: 5.48E-13; mr1819_2 (All); LR P-value: 4.47E-08; mr1860_2 (Jap_All); LR P-value: 4.77E-06; mr1879_2 (Jap_All); LR P-value: 2.13E-08; mr1905_2 (All); LR P-value: 1.22E-08; mr1942_2 (Jap_All); LR P-value: 1.02E-09 |
LOC_Os03g55340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.069; most accessible tissue: Zhenshan97 flag leaf, score: 98.803 |
| vg0331480351 (J) | chr03 | 31480351 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os03g55340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.652; most accessible tissue: Zhenshan97 flag leaf, score: 98.532 |
| vg0331480631 (J) | chr03 | 31480631 | C | A | 99.80% | 0.00% | C -> A,G | NA |
LOC_Os03g55340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g55340.1 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g55330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.976; most accessible tissue: Zhenshan97 flower, score: 95.679 |
| vg0331481016 (J) | chr03 | 31481016 | C | T | 96.50% | 0.00% | C -> T | NA |
LOC_Os03g55340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.313; most accessible tissue: Zhenshan97 flower, score: 93.614 |
| vg0331481079 (J) | chr03 | 31481079 | T | C | 51.50% | 0.04% | T -> C |
mr1050 (All); LR P-value: 2.99E-11;
mr1118 (All); LR P-value: 7.07E-15; mr1272 (All); LR P-value: 2.20E-13; mr1343 (All); LR P-value: 1.85E-07; mr1354 (Ind_All); LR P-value: 1.26E-06; mr1553 (All); LR P-value: 9.36E-12; mr1699 (Ind_All); LMM P-value: 7.43E-06; LR P-value: 1.32E-09; mr1829 (All); LMM P-value: 1.46E-06; LR P-value: 2.15E-12; mr1829 (Ind_All); LMM P-value: 2.81E-07; LR P-value: 1.12E-17; mr1835 (All); LR P-value: 5.57E-06; mr1842 (All); LR P-value: 1.42E-22; mr1842 (Ind_All); LR P-value: 6.61E-12; mr1866 (All); LR P-value: 9.03E-09; mr1902 (All); LR P-value: 1.16E-18; mr1902 (Ind_All); LR P-value: 1.11E-09; mr1979 (All); LR P-value: 2.72E-07; mr1050_2 (All); LR P-value: 2.56E-10; mr1050_2 (Ind_All); LR P-value: 1.88E-06; mr1354_2 (Ind_All); LR P-value: 2.77E-06; mr1531_2 (Ind_All); LR P-value: 1.17E-06; mr1699_2 (Ind_All); LR P-value: 1.72E-11; mr1829_2 (All); LR P-value: 1.15E-14; mr1829_2 (Ind_All); LMM P-value: 7.34E-06; LR P-value: 3.14E-20; mr1842_2 (All); LR P-value: 1.67E-22; mr1842_2 (Ind_All); LR P-value: 3.75E-13; mr1902_2 (All); LR P-value: 6.72E-23; mr1902_2 (Ind_All); LR P-value: 8.88E-16; mr1933_2 (All); LR P-value: 2.55E-25; mr1933_2 (Ind_All); LR P-value: 2.93E-08 |
LOC_Os03g55340.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g55340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.366; most accessible tissue: Zhenshan97 flower, score: 92.816 |
| vg0331481321 (J) | chr03 | 31481321 | C | T | 96.50% | 0.00% | C -> T | NA |
LOC_Os03g55340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.170; most accessible tissue: Callus, score: 90.146 |
| vg0331481556 (J) | chr03 | 31481556 | G | A | 92.80% | 0.00% | G -> A | NA |
LOC_Os03g55340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.388; most accessible tissue: Callus, score: 87.437 |
| vg0331481829 (J) | chr03 | 31481829 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os03g55330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.065; most accessible tissue: Zhenshan97 flower, score: 71.688 |
| vg0331481833 (J) | chr03 | 31481833 | G | A | 55.10% | 0.28% | G -> A |
mr1050 (All); LR P-value: 4.16E-12;
mr1272 (All); LR P-value: 3.38E-13; mr1276 (All); LR P-value: 4.51E-15; mr1278 (All); LR P-value: 2.47E-06; mr1354 (Ind_All); LR P-value: 5.40E-07; mr1680 (All); LR P-value: 4.35E-08; mr1699 (Ind_All); LMM P-value: 1.63E-06; LR P-value: 4.98E-10; mr1829 (All); LR P-value: 2.79E-11; mr1829 (Ind_All); LMM P-value: 7.35E-07; LR P-value: 6.71E-15; mr1835 (All); LR P-value: 4.60E-06; mr1842 (All); LR P-value: 6.58E-23; mr1842 (Ind_All); LMM P-value: 6.53E-06; LR P-value: 3.37E-12; mr1866 (All); LR P-value: 1.47E-08; mr1902 (All); LR P-value: 9.76E-17; mr1902 (Ind_All); LR P-value: 1.38E-07; mr1979 (All); LR P-value: 6.05E-09; mr1050_2 (All); LR P-value: 4.53E-11; mr1050_2 (Ind_All); LR P-value: 1.11E-06; mr1272_2 (All); LR P-value: 4.33E-07; mr1354_2 (Ind_All); LR P-value: 6.15E-07; mr1699_2 (All); LMM P-value: 1.50E-07; LR P-value: 7.25E-29; mr1699_2 (Ind_All); LMM P-value: 7.54E-09; LR P-value: 1.46E-14; mr1829_2 (All); LR P-value: 6.78E-13; mr1829_2 (Ind_All); LR P-value: 3.96E-16; mr1842_2 (All); LR P-value: 6.45E-22; mr1842_2 (Ind_All); LR P-value: 4.16E-12; mr1902_2 (All); LR P-value: 6.30E-21; mr1902_2 (Ind_All); LR P-value: 4.35E-13; mr1933_2 (All); LR P-value: 1.39E-25; mr1933_2 (Ind_All); LR P-value: 2.87E-08 |
LOC_Os03g55330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 46.814; most accessible tissue: Zhenshan97 flower, score: 72.289 |
| vg0331481996 (J) | chr03 | 31481996 | CT | CTTT | 47.90% | 0.47% | CT -> CTTT,C,CTT ,CTTTT | NA |
LOC_Os03g55340.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55340.1 Alt: CTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55330.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g55340.1 Alt: CTTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55330.1 Alt: CTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55340.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55330.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.061; most accessible tissue: Callus, score: 82.658 |
| vg0331482236 (J) | chr03 | 31482236 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os03g55340.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.841; most accessible tissue: Callus, score: 86.387 |
| vg0331482249 (J) | chr03 | 31482249 | A | G | 51.50% | 0.00% | A -> G |
mr1050 (All); LR P-value: 2.05E-11;
mr1118 (All); LR P-value: 4.88E-15; mr1272 (All); LR P-value: 1.14E-13; mr1278 (All); LR P-value: 2.34E-06; mr1343 (All); LR P-value: 9.08E-08; mr1354 (Ind_All); LR P-value: 1.13E-06; mr1553 (All); LR P-value: 1.51E-11; mr1607 (All); LR P-value: 1.59E-08; mr1699 (Ind_All); LR P-value: 6.12E-09; mr1829 (All); LMM P-value: 1.23E-06; LR P-value: 1.92E-12; mr1829 (Ind_All); LMM P-value: 1.87E-07; LR P-value: 3.37E-18; mr1835 (All); LR P-value: 1.88E-06; mr1842 (All); LR P-value: 8.33E-23; mr1842 (Ind_All); LR P-value: 7.42E-12; mr1866 (All); LR P-value: 1.74E-08; mr1902 (All); LR P-value: 1.62E-18; mr1902 (Ind_All); LR P-value: 1.73E-09; mr1933 (All); LR P-value: 4.79E-15; mr1979 (All); LR P-value: 2.45E-07; mr1050_2 (All); LR P-value: 2.70E-11; mr1050_2 (Ind_All); LR P-value: 4.38E-07; mr1118_2 (All); LR P-value: 3.82E-15; mr1272_2 (All); LR P-value: 4.12E-07; mr1354_2 (Ind_All); LR P-value: 3.23E-06; mr1496_2 (All); LR P-value: 3.34E-13; mr1531_2 (Ind_All); LR P-value: 8.42E-07; mr1699_2 (Ind_All); LMM P-value: 3.21E-06; LR P-value: 4.34E-12; mr1829_2 (All); LR P-value: 3.61E-14; mr1829_2 (Ind_All); LR P-value: 1.74E-19; mr1842_2 (All); LR P-value: 1.52E-22; mr1842_2 (Ind_All); LR P-value: 1.31E-12; mr1902_2 (All); LR P-value: 1.49E-22; mr1902_2 (Ind_All); LR P-value: 1.89E-15; mr1933_2 (All); LR P-value: 6.57E-26; mr1933_2 (Ind_All); LR P-value: 8.48E-08 |
LOC_Os03g55340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.741; most accessible tissue: Callus, score: 86.387 |
| vg0331482305 (J) | chr03 | 31482305 | A | C | 51.40% | 0.00% | A -> C |
mr1050 (All); LR P-value: 4.59E-11;
mr1118 (All); LR P-value: 6.16E-15; mr1272 (All); LR P-value: 2.10E-13; mr1278 (All); LR P-value: 1.91E-06; mr1343 (All); LR P-value: 1.08E-07; mr1354 (Ind_All); LR P-value: 1.62E-06; mr1553 (All); LR P-value: 2.64E-11; mr1660 (All); LR P-value: 9.65E-08; mr1680 (All); LR P-value: 2.85E-07; mr1699 (Ind_All); LR P-value: 8.85E-09; mr1829 (All); LMM P-value: 8.91E-07; LR P-value: 2.98E-12; mr1829 (Ind_All); LMM P-value: 6.07E-08; LR P-value: 6.33E-18; mr1835 (All); LR P-value: 2.20E-06; mr1842 (All); LR P-value: 7.40E-23; mr1842 (Ind_All); LR P-value: 4.97E-12; mr1902 (All); LR P-value: 1.18E-17; mr1902 (Ind_All); LR P-value: 2.17E-08; mr1933 (All); LR P-value: 8.68E-15; mr1979 (All); LR P-value: 1.18E-07; mr1050_2 (All); LR P-value: 8.92E-11; mr1050_2 (Ind_All); LR P-value: 1.90E-06; mr1118_2 (All); LR P-value: 7.92E-15; mr1272_2 (All); LR P-value: 1.10E-06; mr1354_2 (Ind_All); LR P-value: 6.79E-06; mr1496_2 (All); LR P-value: 5.55E-13; mr1699_2 (All); LMM P-value: 1.71E-06; LR P-value: 1.66E-28; mr1699_2 (Ind_All); LMM P-value: 1.02E-07; LR P-value: 3.68E-13; mr1829_2 (All); LR P-value: 2.13E-14; mr1829_2 (Ind_All); LMM P-value: 1.32E-06; LR P-value: 3.19E-20; mr1842_2 (All); LR P-value: 3.25E-23; mr1842_2 (Ind_All); LR P-value: 7.50E-14; mr1902_2 (All); LR P-value: 6.94E-23; mr1902_2 (Ind_All); LR P-value: 4.63E-16; mr1933_2 (All); LR P-value: 9.05E-27; mr1933_2 (Ind_All); LR P-value: 1.02E-08 |
LOC_Os03g55340.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.178; most accessible tissue: Zhenshan97 flower, score: 87.040 |
| vg0331482497 (J) | chr03 | 31482497 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os03g55340.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g55330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.682; most accessible tissue: Callus, score: 89.395 |
| vg0331482501 (J) | chr03 | 31482501 | G | A | 96.50% | 0.00% | G -> A | NA |
LOC_Os03g55340.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.025; most accessible tissue: Callus, score: 89.395 |
| vg0331482630 (J) | chr03 | 31482630 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os03g55340.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.023; most accessible tissue: Zhenshan97 flower, score: 84.217 |
| vg0331483064 (J) | chr03 | 31483064 | G | C | 87.80% | 0.00% | C -> G | NA |
LOC_Os03g55340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55350.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.510; most accessible tissue: Callus, score: 86.613 |
| vg0331483111 (J) | chr03 | 31483111 | A | G | 51.40% | 0.15% | A -> G |
mr1050 (All); LR P-value: 1.95E-11;
mr1118 (All); LR P-value: 4.21E-15; mr1272 (All); LR P-value: 1.92E-13; mr1343 (All); LR P-value: 1.43E-07; mr1354 (Ind_All); LR P-value: 1.72E-06; mr1553 (All); LR P-value: 4.01E-11; mr1680 (All); LR P-value: 2.72E-07; mr1699 (Ind_All); LR P-value: 2.32E-09; mr1829 (All); LMM P-value: 1.11E-06; LR P-value: 2.82E-12; mr1829 (Ind_All); LMM P-value: 8.51E-08; LR P-value: 9.94E-18; mr1835 (All); LR P-value: 3.16E-06; mr1842 (All); LR P-value: 4.83E-23; mr1842 (Ind_All); LR P-value: 3.10E-12; mr1902 (All); LR P-value: 3.97E-18; mr1902 (Ind_All); LR P-value: 9.91E-09; mr1933 (All); LR P-value: 7.02E-15; mr1979 (All); LR P-value: 1.67E-07; mr1050_2 (All); LR P-value: 1.59E-10; mr1050_2 (Ind_All); LR P-value: 6.38E-06; mr1118_2 (All); LR P-value: 7.43E-15; mr1272_2 (All); LR P-value: 2.17E-06; mr1354_2 (Ind_All); LR P-value: 5.69E-06; mr1496_2 (All); LR P-value: 4.66E-13; mr1699_2 (Ind_All); LMM P-value: 9.46E-07; LR P-value: 1.52E-12; mr1829_2 (All); LR P-value: 1.27E-14; mr1829_2 (Ind_All); LMM P-value: 4.32E-07; LR P-value: 4.35E-21; mr1842_2 (All); LR P-value: 1.88E-23; mr1842_2 (Ind_All); LR P-value: 1.67E-14; mr1902_2 (All); LR P-value: 6.06E-23; mr1902_2 (Ind_All); LR P-value: 2.44E-16; mr1933_2 (All); LR P-value: 3.16E-27; mr1933_2 (Ind_All); LR P-value: 2.50E-09 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g55340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55350.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.142; most accessible tissue: Zhenshan97 flower, score: 85.807 |
| vg0331483114 (J) | chr03 | 31483114 | A | G | 55.10% | 0.23% | A -> G |
mr1050 (All); LR P-value: 3.41E-12;
mr1272 (All); LR P-value: 4.58E-13; mr1354 (Ind_All); LR P-value: 5.99E-07; mr1680 (All); LR P-value: 3.05E-08; mr1699 (Ind_All); LMM P-value: 2.87E-06; LR P-value: 4.50E-10; mr1829 (All); LR P-value: 1.50E-11; mr1829 (Ind_All); LMM P-value: 4.88E-07; LR P-value: 1.87E-15; mr1835 (All); LR P-value: 3.56E-06; mr1842 (All); LMM P-value: 6.90E-06; LR P-value: 2.63E-23; mr1842 (Ind_All); LMM P-value: 4.03E-06; LR P-value: 9.15E-13; mr1902 (All); LR P-value: 6.65E-17; mr1902 (Ind_All); LR P-value: 1.20E-07; mr1979 (All); LR P-value: 1.33E-08; mr1050_2 (All); LR P-value: 9.02E-11; mr1050_2 (Ind_All); LR P-value: 2.76E-06; mr1272_2 (All); LR P-value: 6.42E-07; mr1354_2 (Ind_All); LR P-value: 7.81E-07; mr1699_2 (All); LMM P-value: 4.34E-07; LR P-value: 6.66E-29; mr1699_2 (Ind_All); LMM P-value: 1.25E-08; LR P-value: 8.35E-15; mr1829_2 (All); LR P-value: 3.35E-13; mr1829_2 (Ind_All); LR P-value: 5.34E-17; mr1842_2 (All); LR P-value: 1.56E-22; mr1842_2 (Ind_All); LR P-value: 3.49E-13; mr1902_2 (All); LR P-value: 5.41E-21; mr1902_2 (Ind_All); LR P-value: 2.62E-13; mr1933_2 (All); LR P-value: 1.54E-26; mr1933_2 (Ind_All); LR P-value: 2.76E-09 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g55340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55350.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.114; most accessible tissue: Zhenshan97 flower, score: 85.885 |
| STR0331482304 (J) | chr03 | 31482304 | CC | CA | 49.00% | 0.00% | CA -> CC | NA |
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