24 variations found. LOC_Os10g02070 (peroxidase precursor; putative; expressed), ranging from 677,085 bp to 678,882 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000677169 (J) | chr10 | 677169 | CT | C | 58.80% | 0.00% | C -> CT | NA |
LOC_Os10g02070.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02080.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.510; most accessible tissue: Minghui63 root, score: 79.298 |
| vg1000677225 (J) | chr10 | 677225 | T | G | 97.20% | 0.00% | T -> G | NA |
LOC_Os10g02070.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.873; most accessible tissue: Zhenshan97 young leaf, score: 78.044 |
| vg1000677277 (J) | chr10 | 677277 | T | A | 83.50% | 0.00% | A -> T |
mr1300 (All); LMM P-value: 1.71E-26; LR P-value: 2.01E-48;
mr1300 (Jap_All); LMM P-value: 8.22E-12; LR P-value: 1.36E-16; mr1310 (All); LMM P-value: 1.43E-29; LR P-value: 1.28E-70; mr1310 (Jap_All); LMM P-value: 1.53E-12; LR P-value: 9.11E-20; mr1498 (All); LMM P-value: 1.43E-06; LR P-value: 1.17E-06; mr1926 (All); LMM P-value: 2.17E-39; LR P-value: 3.55E-87; mr1926 (Jap_All); LMM P-value: 2.95E-14; LR P-value: 1.89E-23; mr1959 (All); LMM P-value: 2.34E-16; LR P-value: 2.92E-22; mr1959 (Jap_All); LMM P-value: 3.24E-09; LR P-value: 1.57E-11; mr1310_2 (All); LMM P-value: 1.42E-45; LR P-value: 4.42E-82; mr1310_2 (Jap_All); LMM P-value: 1.17E-21; LR P-value: 8.88E-34; mr1959_2 (All); LMM P-value: 5.86E-23; LR P-value: 3.56E-34; mr1959_2 (Jap_All); LMM P-value: 3.13E-12; LR P-value: 1.81E-19 |
LOC_Os10g02070.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.419; most accessible tissue: Zhenshan97 young leaf, score: 82.077 |
| vg1000677291 (J) | chr10 | 677291 | C | G | 89.60% | 0.00% | C -> G | NA |
LOC_Os10g02070.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.824; most accessible tissue: Zhenshan97 young leaf, score: 83.199 |
| vg1000677462 (J) | chr10 | 677462 | T | C | 82.00% | 0.00% | C -> T |
mr1011 (Jap_All); LMM P-value: 1.40E-06; LR P-value: 1.40E-06;
mr1156 (All); LR P-value: 6.43E-17; mr1156 (Jap_All); LR P-value: 4.81E-08; mr1163 (Jap_All); LR P-value: 1.80E-08; mr1179 (Jap_All); LR P-value: 9.39E-07; mr1192 (Jap_All); LR P-value: 1.31E-06; mr1252 (Jap_All); LR P-value: 1.45E-06; mr1300 (All); LMM P-value: 2.51E-16; LR P-value: 5.70E-38; mr1300 (Jap_All); LMM P-value: 2.54E-06; LR P-value: 3.81E-10; mr1310 (All); LMM P-value: 1.62E-16; LR P-value: 2.40E-56; mr1310 (Jap_All); LMM P-value: 2.73E-06; LR P-value: 3.53E-12; mr1486 (All); LR P-value: 6.57E-40; mr1486 (Jap_All); LR P-value: 4.93E-12; mr1539 (Jap_All); LR P-value: 6.05E-11; mr1548 (All); LR P-value: 9.09E-23; mr1548 (Jap_All); LR P-value: 1.93E-08; mr1549 (Jap_All); LR P-value: 3.20E-10; mr1570 (Jap_All); LR P-value: 1.30E-07; mr1580 (Jap_All); LR P-value: 8.62E-10; mr1588 (Jap_All); LR P-value: 5.08E-07; mr1624 (All); LR P-value: 3.05E-10; mr1624 (Jap_All); LR P-value: 9.04E-09; mr1723 (Jap_All); LR P-value: 3.00E-07; mr1729 (Jap_All); LR P-value: 5.17E-07; mr1736 (Jap_All); LR P-value: 3.22E-07; mr1740 (Jap_All); LR P-value: 7.66E-06; mr1741 (All); LR P-value: 3.57E-12; mr1757 (Jap_All); LR P-value: 4.92E-09; mr1780 (Jap_All); LR P-value: 7.90E-07; mr1825 (Jap_All); LR P-value: 7.76E-10; mr1870 (Jap_All); LR P-value: 9.59E-07; mr1912 (Jap_All); LR P-value: 4.06E-06; mr1926 (All); LMM P-value: 4.30E-21; LR P-value: 1.51E-66; mr1926 (Jap_All); LMM P-value: 1.04E-06; LR P-value: 1.40E-13; mr1959 (All); LMM P-value: 4.03E-11; LR P-value: 2.61E-17; mr1959 (Jap_All); LR P-value: 3.39E-07; mr1156_2 (All); LR P-value: 3.98E-18; mr1310_2 (All); LMM P-value: 5.08E-18; LR P-value: 3.85E-54; mr1310_2 (Jap_All); LMM P-value: 3.11E-07; LR P-value: 4.77E-15; mr1486_2 (All); LR P-value: 3.66E-49; mr1486_2 (Jap_All); LR P-value: 1.71E-11; mr1563_2 (Jap_All); LR P-value: 1.81E-07; mr1588_2 (Jap_All); LR P-value: 6.04E-06; mr1624_2 (All); LR P-value: 5.02E-09; mr1959_2 (All); LMM P-value: 2.92E-12; LR P-value: 2.30E-24; mr1959_2 (Jap_All); LR P-value: 6.62E-10 |
LOC_Os10g02070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 72.367; most accessible tissue: Zhenshan97 young leaf, score: 88.637 |
| vg1000677463 (J) | chr10 | 677463 | G | T | 82.00% | 0.00% | T -> G |
mr1011 (Jap_All); LMM P-value: 1.40E-06; LR P-value: 1.40E-06;
mr1156 (All); LR P-value: 6.43E-17; mr1156 (Jap_All); LR P-value: 4.81E-08; mr1163 (Jap_All); LR P-value: 1.80E-08; mr1179 (Jap_All); LR P-value: 9.39E-07; mr1192 (Jap_All); LR P-value: 1.31E-06; mr1252 (Jap_All); LR P-value: 1.45E-06; mr1300 (All); LMM P-value: 2.51E-16; LR P-value: 5.70E-38; mr1300 (Jap_All); LMM P-value: 2.54E-06; LR P-value: 3.81E-10; mr1310 (All); LMM P-value: 1.62E-16; LR P-value: 2.40E-56; mr1310 (Jap_All); LMM P-value: 2.73E-06; LR P-value: 3.53E-12; mr1486 (All); LR P-value: 6.57E-40; mr1486 (Jap_All); LR P-value: 4.93E-12; mr1539 (Jap_All); LR P-value: 6.05E-11; mr1548 (All); LR P-value: 9.09E-23; mr1548 (Jap_All); LR P-value: 1.93E-08; mr1549 (Jap_All); LR P-value: 3.20E-10; mr1570 (Jap_All); LR P-value: 1.30E-07; mr1580 (Jap_All); LR P-value: 8.62E-10; mr1588 (Jap_All); LR P-value: 5.08E-07; mr1624 (All); LR P-value: 3.05E-10; mr1624 (Jap_All); LR P-value: 9.04E-09; mr1723 (Jap_All); LR P-value: 3.00E-07; mr1729 (Jap_All); LR P-value: 5.17E-07; mr1736 (Jap_All); LR P-value: 3.22E-07; mr1740 (Jap_All); LR P-value: 7.66E-06; mr1741 (All); LR P-value: 3.57E-12; mr1757 (Jap_All); LR P-value: 4.92E-09; mr1780 (Jap_All); LR P-value: 7.90E-07; mr1825 (Jap_All); LR P-value: 7.76E-10; mr1870 (Jap_All); LR P-value: 9.59E-07; mr1912 (Jap_All); LR P-value: 4.06E-06; mr1926 (All); LMM P-value: 4.30E-21; LR P-value: 1.51E-66; mr1926 (Jap_All); LMM P-value: 1.04E-06; LR P-value: 1.40E-13; mr1959 (All); LMM P-value: 4.03E-11; LR P-value: 2.61E-17; mr1959 (Jap_All); LR P-value: 3.39E-07; mr1156_2 (All); LR P-value: 3.98E-18; mr1310_2 (All); LMM P-value: 5.08E-18; LR P-value: 3.85E-54; mr1310_2 (Jap_All); LMM P-value: 3.11E-07; LR P-value: 4.77E-15; mr1486_2 (All); LR P-value: 3.66E-49; mr1486_2 (Jap_All); LR P-value: 1.71E-11; mr1563_2 (Jap_All); LR P-value: 1.81E-07; mr1588_2 (Jap_All); LR P-value: 6.04E-06; mr1624_2 (All); LR P-value: 5.02E-09; mr1959_2 (All); LMM P-value: 2.92E-12; LR P-value: 2.30E-24; mr1959_2 (Jap_All); LR P-value: 6.62E-10 |
LOC_Os10g02070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.325; most accessible tissue: Zhenshan97 young leaf, score: 88.637 |
| vg1000677523 (J) | chr10 | 677523 | G | A | 53.30% | 0.25% | G -> A |
Grain_length (All); LR P-value: 8.87E-16;
mr1011 (Jap_All); LMM P-value: 1.99E-06; LR P-value: 1.99E-06; mr1042 (All); LR P-value: 5.12E-06; mr1043 (All); LR P-value: 5.54E-06; mr1156 (Jap_All); LR P-value: 1.19E-07; mr1163 (Jap_All); LR P-value: 1.67E-08; mr1179 (Jap_All); LR P-value: 2.07E-06; mr1192 (All); LR P-value: 1.98E-07; mr1192 (Jap_All); LR P-value: 5.07E-07; mr1251 (Jap_All); LR P-value: 1.84E-09; mr1280 (All); LR P-value: 2.72E-06; mr1300 (Jap_All); LMM P-value: 5.23E-06; LR P-value: 5.05E-10; mr1310 (Jap_All); LMM P-value: 9.07E-06; LR P-value: 9.12E-12; mr1318 (All); LR P-value: 1.31E-06; mr1328 (All); LR P-value: 6.80E-08; mr1479 (All); LR P-value: 2.56E-07; mr1486 (Jap_All); LR P-value: 2.00E-12; mr1502 (All); LR P-value: 3.47E-06; mr1520 (All); LR P-value: 8.85E-06; mr1539 (All); LR P-value: 4.62E-11; mr1539 (Jap_All); LR P-value: 2.77E-11; mr1548 (Jap_All); LR P-value: 2.02E-08; mr1549 (Jap_All); LR P-value: 5.82E-10; mr1563 (Jap_All); LR P-value: 5.75E-09; mr1570 (Jap_All); LR P-value: 3.23E-07; mr1576 (All); LR P-value: 3.63E-07; mr1580 (Jap_All); LR P-value: 1.37E-10; mr1588 (Jap_All); LR P-value: 1.12E-06; mr1614 (All); LR P-value: 4.41E-06; mr1621 (All); LR P-value: 6.45E-06; mr1624 (Jap_All); LR P-value: 1.79E-08; mr1736 (Jap_All); LR P-value: 5.16E-07; mr1757 (Jap_All); LR P-value: 1.06E-08; mr1769 (All); LR P-value: 1.64E-09; mr1780 (Jap_All); LR P-value: 2.31E-06; mr1825 (Jap_All); LR P-value: 2.68E-10; mr1870 (Jap_All); LR P-value: 5.00E-08; mr1912 (All); LR P-value: 1.78E-07; mr1912 (Jap_All); LR P-value: 1.84E-06; mr1926 (Jap_All); LMM P-value: 6.64E-06; LR P-value: 9.84E-13; mr1951 (All); LR P-value: 1.08E-06; mr1959 (Jap_All); LR P-value: 8.46E-07; mr1975 (All); LR P-value: 4.48E-07; mr1976 (All); LR P-value: 1.17E-06; mr1156_2 (Jap_All); LR P-value: 1.38E-07; mr1310_2 (Jap_All); LMM P-value: 1.38E-06; LR P-value: 1.60E-14; mr1354_2 (Jap_All); LR P-value: 8.89E-06; mr1486_2 (Jap_All); LR P-value: 6.11E-12; mr1563_2 (Jap_All); LR P-value: 3.89E-08; mr1588_2 (Jap_All); LR P-value: 5.68E-06; mr1959_2 (Jap_All); LR P-value: 1.13E-09 |
LOC_Os10g02070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g02070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.305; most accessible tissue: Zhenshan97 young leaf, score: 90.547 |
| vg1000677660 (J) | chr10 | 677660 | C | A | 97.50% | 0.00% | C -> A | NA |
LOC_Os10g02070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.180; most accessible tissue: Zhenshan97 young leaf, score: 88.759 |
| vg1000677692 (J) | chr10 | 677692 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os10g02070.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os10g02080.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.100; most accessible tissue: Zhenshan97 young leaf, score: 87.584 |
| vg1000677783 (J) | chr10 | 677783 | A | G | 98.10% | 0.00% | A -> G | NA |
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.356; most accessible tissue: Zhenshan97 young leaf, score: 86.055 |
| vg1000677787 (J) | chr10 | 677787 | C | T | 98.10% | 0.00% | C -> T | NA |
LOC_Os10g02080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.458; most accessible tissue: Zhenshan97 young leaf, score: 85.715 |
| vg1000677801 (J) | chr10 | 677801 | A | T | 98.10% | 0.00% | A -> T | NA |
LOC_Os10g02080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.988; most accessible tissue: Zhenshan97 young leaf, score: 85.715 |
| vg1000677806 (J) | chr10 | 677806 | A | T | 98.10% | 0.00% | A -> T | NA |
LOC_Os10g02080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.671; most accessible tissue: Zhenshan97 young leaf, score: 85.886 |
| vg1000677809 (J) | chr10 | 677809 | A | G | 98.10% | 0.00% | A -> G | NA |
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.427; most accessible tissue: Zhenshan97 young leaf, score: 86.055 |
| vg1000677810 (J) | chr10 | 677810 | A | G | 98.10% | 0.00% | A -> G | NA |
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.427; most accessible tissue: Zhenshan97 young leaf, score: 86.055 |
| vg1000677878 (J) | chr10 | 677878 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os10g02070.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.974; most accessible tissue: Zhenshan97 young leaf, score: 85.001 |
| vg1000678017 (J) | chr10 | 678017 | G | C | 89.70% | 0.00% | G -> C | NA |
LOC_Os10g02080.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.301; most accessible tissue: Zhenshan97 young leaf, score: 84.814 |
| vg1000678603 (J) | chr10 | 678603 | G | A | 97.40% | 0.00% | G -> A | NA |
LOC_Os10g02080.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02070.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.074; most accessible tissue: Minghui63 root, score: 87.125 |
| vg1000678662 (J) | chr10 | 678662 | A | G | 97.40% | 0.00% | A -> G | NA |
LOC_Os10g02070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.541; most accessible tissue: Minghui63 root, score: 89.304 |
| vg1000678767 (J) | chr10 | 678767 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os10g02070.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.288; most accessible tissue: Minghui63 root, score: 92.151 |
| vg1000678800 (J) | chr10 | 678800 | T | A | 83.50% | 0.00% | A -> T |
mr1300 (All); LMM P-value: 4.89E-25; LR P-value: 6.50E-47;
mr1300 (Jap_All); LMM P-value: 8.22E-12; LR P-value: 1.36E-16; mr1310 (All); LMM P-value: 6.58E-28; LR P-value: 1.74E-68; mr1310 (Jap_All); LMM P-value: 1.53E-12; LR P-value: 9.11E-20; mr1498 (All); LMM P-value: 4.46E-06; mr1926 (All); LMM P-value: 4.43E-37; LR P-value: 3.74E-84; mr1926 (Jap_All); LMM P-value: 2.95E-14; LR P-value: 1.89E-23; mr1959 (All); LMM P-value: 4.20E-15; LR P-value: 4.74E-21; mr1959 (Jap_All); LMM P-value: 3.24E-09; LR P-value: 1.57E-11; mr1310_2 (All); LMM P-value: 1.28E-43; LR P-value: 9.12E-80; mr1310_2 (Jap_All); LMM P-value: 1.17E-21; LR P-value: 8.88E-34; mr1959_2 (All); LMM P-value: 1.30E-21; LR P-value: 7.88E-33; mr1959_2 (Jap_All); LMM P-value: 3.13E-12; LR P-value: 1.81E-19 |
LOC_Os10g02070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.992; most accessible tissue: Minghui63 root, score: 93.695 |
| vg1000678811 (J) | chr10 | 678811 | G | C | 96.10% | 0.00% | G -> C | NA |
LOC_Os10g02070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.237; most accessible tissue: Minghui63 root, score: 93.736 |
| vg1000678859 (J) | chr10 | 678859 | GC | G | 98.00% | 0.00% | GC -> G | NA |
LOC_Os10g02070.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g02080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.098; most accessible tissue: Minghui63 root, score: 93.861 |
| STR1000677170 (J) | chr10 | 677170 | TT | T | 60.60% | 0.00% | T -> TT | NA |
|