24 variations found. LOC_Os07g47270 (protein kinase APK1B; chloroplast precursor; putative; expressed), ranging from 28,250,041 bp to 28,253,666 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0728250113 (J) | chr07 | 28250113 | A | G | 98.20% | 0.00% | A -> G | NA |
LOC_Os07g47270.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47250.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47250.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47250.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.003; most accessible tissue: Minghui63 flower, score: 70.849 |
| vg0728250406 (J) | chr07 | 28250406 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os07g47270.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g47250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g47250.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g47250.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.490; most accessible tissue: Zhenshan97 young leaf, score: 78.347 |
| vg0728250569 (J) | chr07 | 28250569 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os07g47270.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g47260.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.247; most accessible tissue: Callus, score: 82.164 |
| vg0728250615 (J) | chr07 | 28250615 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os07g47270.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.402; most accessible tissue: Zhenshan97 young leaf, score: 81.600 |
| vg0728250650 (J) | chr07 | 28250650 | C | T | 54.80% | 0.70% | C -> T |
Grain_width (Jap_All); LR P-value: 7.06E-12;
mr1077 (Jap_All); LR P-value: 6.37E-06; mr1124 (Jap_All); LR P-value: 4.96E-07; mr1277 (Jap_All); LR P-value: 4.62E-07; mr1551 (Jap_All); LR P-value: 9.20E-08; mr1671 (Jap_All); LR P-value: 1.62E-06; mr1789 (Jap_All); LR P-value: 5.00E-13; mr1879 (Jap_All); LR P-value: 5.29E-14; mr1304_2 (Jap_All); LR P-value: 4.08E-10; mr1308_2 (Jap_All); LR P-value: 8.36E-08; mr1347_2 (Jap_All); LR P-value: 3.60E-07; mr1361_2 (Jap_All); LR P-value: 8.23E-10; mr1368_2 (Jap_All); LR P-value: 2.58E-13; mr1401_2 (Jap_All); LR P-value: 2.73E-07; mr1540_2 (Jap_All); LR P-value: 5.19E-15; mr1551_2 (Jap_All); LR P-value: 1.19E-07; mr1584_2 (Jap_All); LR P-value: 4.39E-11; mr1730_2 (Jap_All); LR P-value: 1.62E-06; mr1732_2 (Jap_All); LR P-value: 1.12E-14; mr1853_2 (Jap_All); LR P-value: 9.65E-06; mr1866_2 (Jap_All); LR P-value: 1.47E-06; mr1879_2 (Jap_All); LR P-value: 1.23E-10; mr1942_2 (Jap_All); LR P-value: 7.02E-10 |
LOC_Os07g47270.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g47270.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 61.341; most accessible tissue: Zhenshan97 young leaf, score: 78.044 |
| vg0728250817 (J) | chr07 | 28250817 | A | G | 53.00% | 0.28% | A -> G |
mr1075 (Jap_All); LR P-value: 7.19E-06;
mr1124 (Jap_All); LR P-value: 2.53E-06; mr1277 (Jap_All); LR P-value: 2.42E-06; mr1551 (Jap_All); LR P-value: 1.37E-07; mr1584 (Jap_All); LR P-value: 6.30E-07; mr1879 (Jap_All); LR P-value: 1.06E-13; mr1304_2 (Jap_All); LR P-value: 1.01E-08; mr1308_2 (Jap_All); LR P-value: 1.40E-07; mr1361_2 (Jap_All); LR P-value: 2.82E-09; mr1368_2 (Jap_All); LR P-value: 1.50E-12; mr1540_2 (Jap_All); LR P-value: 3.67E-15; mr1584_2 (Jap_All); LR P-value: 2.96E-10; mr1629_2 (Jap_All); LR P-value: 1.57E-06; mr1730_2 (Jap_All); LR P-value: 2.79E-06; mr1732_2 (Jap_All); LR P-value: 3.07E-14; mr1866_2 (Jap_All); LR P-value: 2.02E-06; mr1879_2 (Jap_All); LR P-value: 2.10E-10; mr1942_2 (Jap_All); LR P-value: 3.97E-10 |
LOC_Os07g47270.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g47270.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 60.740; most accessible tissue: Callus, score: 81.802 |
| vg0728251061 (J) | chr07 | 28251061 | G | T | 98.90% | 0.00% | G -> T | NA |
LOC_Os07g47270.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 59.502; most accessible tissue: Callus, score: 83.022 |
| vg0728251148 (J) | chr07 | 28251148 | G | A | 55.00% | 0.59% | G -> A |
Grain_width (Jap_All); LR P-value: 7.06E-12;
mr1077 (Jap_All); LR P-value: 6.37E-06; mr1124 (Jap_All); LR P-value: 4.96E-07; mr1277 (Jap_All); LR P-value: 4.62E-07; mr1551 (Jap_All); LR P-value: 9.20E-08; mr1671 (Jap_All); LR P-value: 1.62E-06; mr1789 (Jap_All); LR P-value: 5.00E-13; mr1879 (Jap_All); LR P-value: 5.29E-14; mr1304_2 (Jap_All); LR P-value: 4.08E-10; mr1308_2 (Jap_All); LR P-value: 8.36E-08; mr1347_2 (Jap_All); LR P-value: 3.60E-07; mr1361_2 (Jap_All); LR P-value: 8.23E-10; mr1368_2 (Jap_All); LR P-value: 2.58E-13; mr1401_2 (Jap_All); LR P-value: 2.73E-07; mr1540_2 (Jap_All); LR P-value: 5.19E-15; mr1551_2 (Jap_All); LR P-value: 1.19E-07; mr1584_2 (Jap_All); LR P-value: 4.39E-11; mr1730_2 (Jap_All); LR P-value: 1.62E-06; mr1732_2 (Jap_All); LR P-value: 1.12E-14; mr1853_2 (Jap_All); LR P-value: 9.65E-06; mr1866_2 (Jap_All); LR P-value: 1.47E-06; mr1879_2 (Jap_All); LR P-value: 1.23E-10; mr1942_2 (Jap_All); LR P-value: 7.02E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g47260.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.678; most accessible tissue: Minghui63 flag leaf, score: 70.648 |
| vg0728251149 (J) | chr07 | 28251149 | A | T | 55.00% | 0.59% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.678; most accessible tissue: Minghui63 flag leaf, score: 70.648 |
| vg0728251275 (J) | chr07 | 28251275 | T | C | 52.90% | 0.44% | T -> C |
mr1075 (Jap_All); LR P-value: 7.43E-06;
mr1077 (Jap_All); LR P-value: 9.77E-06; mr1124 (Jap_All); LR P-value: 9.70E-07; mr1277 (Jap_All); LR P-value: 9.27E-07; mr1551 (Jap_All); LR P-value: 1.15E-07; mr1879 (Jap_All); LR P-value: 4.10E-14; mr1304_2 (Jap_All); LR P-value: 1.22E-09; mr1308_2 (Jap_All); LR P-value: 3.43E-08; mr1361_2 (Jap_All); LR P-value: 1.33E-09; mr1368_2 (Jap_All); LR P-value: 3.82E-13; mr1449_2 (Jap_All); LR P-value: 7.80E-06; mr1540_2 (Jap_All); LR P-value: 8.04E-16; mr1551_2 (Jap_All); LR P-value: 3.07E-07; mr1584_2 (Jap_All); LR P-value: 5.03E-11; mr1730_2 (Jap_All); LR P-value: 1.55E-06; mr1732_2 (Jap_All); LR P-value: 2.83E-15; mr1853_2 (Jap_All); LR P-value: 5.63E-06; mr1866_2 (Jap_All); LR P-value: 1.09E-06; mr1879_2 (Jap_All); LR P-value: 4.33E-11; mr1942_2 (Jap_All); LR P-value: 1.62E-10 |
LOC_Os07g47270.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g47270.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 55.702; most accessible tissue: Callus, score: 81.863 |
| vg0728251572 (J) | chr07 | 28251572 | C | G | 98.20% | 0.00% | C -> G | NA |
LOC_Os07g47270.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 48.707; most accessible tissue: Callus, score: 75.477 |
| vg0728251632 (J) | chr07 | 28251632 | G | C | 98.20% | 0.00% | G -> C | NA |
LOC_Os07g47270.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 45.137; most accessible tissue: Minghui63 flag leaf, score: 60.569 |
| vg0728251931 (J) | chr07 | 28251931 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.574; most accessible tissue: Callus, score: 78.833 |
| vg0728252439 (J) | chr07 | 28252439 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os07g47270.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.184; most accessible tissue: Callus, score: 70.454 |
| vg0728252640 (J) | chr07 | 28252640 | A | G | 96.90% | 0.00% | A -> G |
mr1114 (Jap_All); LR P-value: 7.14E-07;
mr1117 (Jap_All); LR P-value: 3.86E-08; mr1118 (Jap_All); LR P-value: 1.30E-06; mr1496 (Jap_All); LR P-value: 8.79E-07; mr1113_2 (Jap_All); LR P-value: 2.85E-06; mr1114_2 (Jap_All); LR P-value: 1.95E-06; mr1117_2 (Jap_All); LR P-value: 1.10E-09; mr1119_2 (Jap_All); LR P-value: 5.40E-08; mr1120_2 (Jap_All); LR P-value: 3.77E-06; mr1240_2 (Jap_All); LR P-value: 7.97E-07; mr1242_2 (Jap_All); LR P-value: 9.23E-07; mr1247_2 (Jap_All); LR P-value: 2.12E-06; mr1496_2 (Jap_All); LR P-value: 1.03E-09; mr1691_2 (Jap_All); LR P-value: 1.87E-06; mr1720_2 (Jap_All); LR P-value: 2.27E-06; mr1745_2 (Jap_All); LR P-value: 1.72E-06 |
LOC_Os07g47260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.187; most accessible tissue: Zhenshan97 root, score: 72.671 |
| vg0728252659 (J) | chr07 | 28252659 | A | C | 99.80% | 0.00% | A -> C | NA |
LOC_Os07g47260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g47270.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 50.903; most accessible tissue: Zhenshan97 root, score: 73.600 |
| vg0728252688 (J) | chr07 | 28252688 | A | T | 53.00% | 0.53% | A -> T |
Grain_width (Jap_All); LR P-value: 7.06E-12;
mr1077 (Jap_All); LR P-value: 6.37E-06; mr1124 (Jap_All); LR P-value: 4.96E-07; mr1277 (Jap_All); LR P-value: 4.62E-07; mr1551 (Jap_All); LR P-value: 9.20E-08; mr1671 (Jap_All); LR P-value: 1.62E-06; mr1789 (Jap_All); LR P-value: 5.00E-13; mr1879 (Jap_All); LR P-value: 5.29E-14; mr1304_2 (Jap_All); LR P-value: 4.08E-10; mr1308_2 (Jap_All); LR P-value: 8.36E-08; mr1347_2 (Jap_All); LR P-value: 3.60E-07; mr1361_2 (Jap_All); LR P-value: 8.23E-10; mr1364_2 (All); LR P-value: 6.27E-08; mr1368_2 (Jap_All); LR P-value: 2.58E-13; mr1401_2 (Jap_All); LR P-value: 2.73E-07; mr1540_2 (Jap_All); LR P-value: 5.19E-15; mr1551_2 (Jap_All); LR P-value: 1.19E-07; mr1584_2 (Jap_All); LR P-value: 4.39E-11; mr1730_2 (Jap_All); LR P-value: 1.62E-06; mr1732_2 (Jap_All); LR P-value: 1.12E-14; mr1853_2 (Jap_All); LR P-value: 9.65E-06; mr1866_2 (Jap_All); LR P-value: 1.47E-06; mr1879_2 (Jap_All); LR P-value: 1.23E-10; mr1942_2 (Jap_All); LR P-value: 7.02E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.953; most accessible tissue: Callus, score: 77.588 |
| vg0728252744 (J) | chr07 | 28252744 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.776; most accessible tissue: Callus, score: 77.588 |
| vg0728252961 (J) | chr07 | 28252961 | C | T | 98.20% | 0.00% | C -> T | NA |
LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.313; most accessible tissue: Callus, score: 80.411 |
| vg0728253428 (J) | chr07 | 28253428 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os07g47270.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g47280.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g47260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.865; most accessible tissue: Callus, score: 97.240 |
| vg0728253456 (J) | chr07 | 28253456 | T | C | 98.20% | 0.00% | T -> C | NA |
LOC_Os07g47270.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g47280.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.385; most accessible tissue: Callus, score: 97.240 |
| vg0728253493 (J) | chr07 | 28253493 | T | C | 55.00% | 0.34% | T -> C |
Grain_width (Jap_All); LR P-value: 7.06E-12;
mr1077 (Jap_All); LR P-value: 6.37E-06; mr1124 (Jap_All); LR P-value: 4.96E-07; mr1277 (Jap_All); LR P-value: 4.62E-07; mr1551 (Jap_All); LR P-value: 9.20E-08; mr1671 (Jap_All); LR P-value: 1.62E-06; mr1789 (Jap_All); LR P-value: 5.00E-13; mr1879 (Jap_All); LR P-value: 5.29E-14; mr1304_2 (Jap_All); LR P-value: 4.08E-10; mr1308_2 (Jap_All); LR P-value: 8.36E-08; mr1347_2 (Jap_All); LR P-value: 3.60E-07; mr1361_2 (Jap_All); LR P-value: 8.23E-10; mr1368_2 (Jap_All); LR P-value: 2.58E-13; mr1401_2 (Jap_All); LR P-value: 2.73E-07; mr1540_2 (Jap_All); LR P-value: 5.19E-15; mr1551_2 (Jap_All); LR P-value: 1.19E-07; mr1584_2 (Jap_All); LR P-value: 4.39E-11; mr1730_2 (Jap_All); LR P-value: 1.62E-06; mr1732_2 (Jap_All); LR P-value: 1.12E-14; mr1853_2 (Jap_All); LR P-value: 9.65E-06; mr1866_2 (Jap_All); LR P-value: 1.47E-06; mr1879_2 (Jap_All); LR P-value: 1.23E-10; mr1942_2 (Jap_All); LR P-value: 7.02E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47280.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.804; most accessible tissue: Callus, score: 97.240 |
| vg0728253524 (J) | chr07 | 28253524 | G | T | 53.10% | 0.13% | G -> T |
mr1075 (Jap_All); LR P-value: 7.43E-06;
mr1077 (Jap_All); LR P-value: 9.77E-06; mr1124 (Jap_All); LR P-value: 9.70E-07; mr1277 (Jap_All); LR P-value: 9.27E-07; mr1551 (Jap_All); LR P-value: 1.15E-07; mr1879 (Jap_All); LR P-value: 4.10E-14; mr1304_2 (Jap_All); LR P-value: 1.22E-09; mr1308_2 (Jap_All); LR P-value: 3.43E-08; mr1361_2 (Jap_All); LR P-value: 1.33E-09; mr1368_2 (Jap_All); LR P-value: 3.82E-13; mr1449_2 (Jap_All); LR P-value: 7.80E-06; mr1540_2 (Jap_All); LR P-value: 8.04E-16; mr1551_2 (Jap_All); LR P-value: 3.07E-07; mr1584_2 (Jap_All); LR P-value: 5.03E-11; mr1730_2 (Jap_All); LR P-value: 1.55E-06; mr1732_2 (Jap_All); LR P-value: 2.83E-15; mr1853_2 (Jap_All); LR P-value: 5.63E-06; mr1866_2 (Jap_All); LR P-value: 1.09E-06; mr1879_2 (Jap_All); LR P-value: 4.33E-11; mr1942_2 (Jap_All); LR P-value: 1.62E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g47270.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g47260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.126; most accessible tissue: Callus, score: 97.240 |
| vg0728253578 (J) | chr07 | 28253578 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os07g47270.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g47280.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g47260.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.020; most accessible tissue: Callus, score: 95.977 |