21 variations found. LOC_Os05g30820 (protein kinase; putative; expressed), ranging from 17,885,533 bp to 17,888,972 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0517885731 (J) | chr05 | 17885731 | TA | T | 64.40% | 0.36% | T -> TA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.124; most accessible tissue: Callus, score: 82.543 |
| vg0517885764 (J) | chr05 | 17885764 | A | G | 64.50% | 0.40% | G -> A |
mr1044 (All); LR P-value: 2.53E-06;
mr1044 (Ind_All); LR P-value: 2.70E-06; mr1069 (All); LR P-value: 8.05E-12; mr1133 (All); LR P-value: 1.86E-18; mr1202 (All); LR P-value: 1.57E-29; mr1842 (All); LR P-value: 2.33E-17; mr1902 (All); LR P-value: 1.46E-12; mr1072_2 (All); LR P-value: 4.07E-38; mr1654_2 (All); LR P-value: 3.56E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.196; most accessible tissue: Callus, score: 82.543 |
| vg0517885916 (J) | chr05 | 17885916 | C | T | 98.60% | 0.00% | C -> T | NA |
LOC_Os05g30820.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.450; most accessible tissue: Zhenshan97 flower, score: 77.755 |
| vg0517886408 (J) | chr05 | 17886408 | GAA | GA | 72.00% | 0.00% | GAA -> GA,G,GAAA | NA |
LOC_Os05g30810.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30810.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.385; most accessible tissue: Minghui63 flower, score: 89.033 |
| vg0517886449 (J) | chr05 | 17886449 | G | A | 64.70% | 0.04% | A -> G |
mr1044 (Ind_All); LR P-value: 2.70E-06;
mr1069 (All); LR P-value: 7.42E-12; mr1075 (All); LR P-value: 1.88E-28; mr1133 (All); LR P-value: 1.12E-18; mr1202 (All); LR P-value: 1.05E-29; mr1842 (All); LR P-value: 9.97E-17; mr1902 (All); LR P-value: 3.51E-12; mr1072_2 (All); LR P-value: 2.47E-38; mr1654_2 (All); LR P-value: 1.58E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g30810.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.279; most accessible tissue: Minghui63 flower, score: 89.149 |
| vg0517886498 (J) | chr05 | 17886498 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os05g30820.2 Alt: T| splice_region_variant LOW(snpEff)
LOC_Os05g30820.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g30810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g30810.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g30820.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.541; most accessible tissue: Minghui63 flower, score: 88.913 |
| vg0517886506 (J) | chr05 | 17886506 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os05g30820.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g30810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g30810.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g30820.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.848; most accessible tissue: Minghui63 flower, score: 89.206 |
| vg0517886668 (J) | chr05 | 17886668 | G | T | 76.00% | 0.00% | G -> T |
mr1044 (Ind_All); LR P-value: 7.19E-07;
mr1415 (Ind_All); LR P-value: 6.02E-06; mr1482 (Ind_All); LR P-value: 6.10E-06; mr1567 (Ind_All); LR P-value: 6.02E-06; mr1002_2 (Ind_All); LR P-value: 7.76E-06; mr1167_2 (Ind_All); LR P-value: 8.47E-07; mr1181_2 (Jap_All); LMM P-value: 9.27E-06; LR P-value: 9.26E-06; mr1408_2 (All); LR P-value: 1.23E-08 |
LOC_Os05g30820.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30810.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.135; most accessible tissue: Minghui63 flower, score: 87.461 |
| vg0517887044 (J) | chr05 | 17887044 | A | C | 89.00% | 0.00% | C -> A |
Grain_length (All); LR P-value: 4.15E-14;
mr1011 (All); LR P-value: 5.97E-06; mr1163 (Jap_All); LR P-value: 1.71E-07; mr1182 (All); LR P-value: 1.58E-11; mr1486 (Jap_All); LR P-value: 2.60E-10; mr1543 (All); LR P-value: 9.04E-06; mr1543 (Jap_All); LR P-value: 7.93E-07; mr1629 (Jap_All); LR P-value: 2.71E-06; mr1650 (All); LR P-value: 3.85E-12; mr1658 (All); LR P-value: 1.05E-08; mr1182_2 (Jap_All); LR P-value: 2.43E-06 |
LOC_Os05g30810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30810.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.292; most accessible tissue: Callus, score: 75.168 |
| vg0517887151 (J) | chr05 | 17887151 | C | T | 64.70% | 0.00% | T -> C |
mr1044 (Ind_All); LR P-value: 1.64E-06;
mr1069 (All); LR P-value: 1.87E-12; mr1075 (All); LR P-value: 7.86E-29; mr1077 (Ind_All); LR P-value: 1.40E-06; mr1133 (All); LR P-value: 2.94E-18; mr1202 (All); LR P-value: 3.00E-30; mr1415 (Ind_All); LR P-value: 6.54E-06; mr1567 (Ind_All); LR P-value: 6.54E-06; mr1667 (All); LR P-value: 9.37E-12; mr1842 (All); LR P-value: 9.23E-17; mr1902 (All); LR P-value: 5.51E-12; mr1002_2 (Ind_All); LR P-value: 5.36E-06; mr1072_2 (All); LR P-value: 6.81E-40; mr1075_2 (All); LR P-value: 4.47E-37; mr1654_2 (All); LR P-value: 3.04E-07; mr1861_2 (All); LR P-value: 1.01E-47 |
LOC_Os05g30820.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os05g30820.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 50.947; most accessible tissue: Zhenshan97 panicle, score: 65.386 |
| vg0517887386 (J) | chr05 | 17887386 | T | TA | 64.80% | 0.00% | TA -> T,TAA | NA |
LOC_Os05g30830.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.457; most accessible tissue: Callus, score: 67.262 |
| vg0517887639 (J) | chr05 | 17887639 | T | C | 64.60% | 0.00% | C -> T |
mr1039 (Ind_All); LR P-value: 5.20E-07;
mr1044 (All); LR P-value: 7.65E-07; mr1044 (Ind_All); LR P-value: 1.47E-06; mr1069 (All); LR P-value: 1.14E-11; mr1133 (All); LR P-value: 2.36E-19; mr1399 (Ind_All); LR P-value: 9.96E-07; mr1482 (Ind_All); LR P-value: 9.81E-06; mr1667 (All); LR P-value: 1.89E-12; mr1842 (All); LR P-value: 3.61E-16; mr1902 (All); LR P-value: 5.20E-12; mr1002_2 (Ind_All); LR P-value: 7.91E-07; mr1039_2 (Ind_All); LR P-value: 2.64E-07; mr1133_2 (All); LR P-value: 1.34E-14; mr1399_2 (Ind_All); LR P-value: 6.24E-06; mr1654_2 (All); LR P-value: 2.86E-07 |
LOC_Os05g30820.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g30820.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 58.027; most accessible tissue: Callus, score: 74.844 |
| vg0517887899 (J) | chr05 | 17887899 | T | G | 64.50% | 0.00% | G -> T |
mr1044 (All); LR P-value: 1.71E-06;
mr1044 (Ind_All); LR P-value: 5.82E-06; mr1069 (All); LR P-value: 6.61E-12; mr1133 (All); LR P-value: 5.59E-19; mr1202 (All); LR P-value: 1.44E-29; mr1667 (All); LR P-value: 2.99E-12; mr1842 (All); LR P-value: 1.47E-17; mr1902 (All); LR P-value: 4.06E-12; mr1072_2 (All); LR P-value: 3.18E-39; mr1568_2 (All); LR P-value: 5.00E-07; mr1654_2 (All); LR P-value: 2.08E-07; mr1790_2 (All); LR P-value: 2.39E-14; mr1933_2 (All); LR P-value: 4.73E-22 |
LOC_Os05g30830.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.065; most accessible tissue: Zhenshan97 flower, score: 76.751 |
| vg0517887964 (J) | chr05 | 17887964 | T | C | 64.70% | 0.00% | C -> T |
mr1044 (All); LR P-value: 9.34E-07;
mr1044 (Ind_All); LR P-value: 7.16E-07; mr1069 (All); LR P-value: 2.92E-12; mr1077 (Ind_All); LR P-value: 3.56E-06; mr1133 (All); LR P-value: 3.03E-18; mr1202 (All); LR P-value: 1.73E-29; mr1415 (Ind_All); LR P-value: 5.25E-06; mr1482 (Ind_All); LR P-value: 6.89E-06; mr1567 (Ind_All); LR P-value: 5.25E-06; mr1842 (All); LR P-value: 1.28E-16; mr1902 (All); LR P-value: 2.41E-12; mr1002_2 (Ind_All); LR P-value: 9.17E-06; mr1072_2 (All); LR P-value: 1.36E-37; mr1654_2 (All); LR P-value: 5.56E-07; mr1756_2 (All); LR P-value: 7.13E-10 |
LOC_Os05g30830.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.001; most accessible tissue: Callus, score: 83.529 |
| vg0517888098 (J) | chr05 | 17888098 | TA | T | 87.70% | 0.00% | T -> TA,TAA | NA |
LOC_Os05g30830.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 |
| vg0517888122 (J) | chr05 | 17888122 | TC | T | 57.90% | 0.00% | T -> TC,TCC,TCC C | NA |
LOC_Os05g30830.1 Alt: TCCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: TCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 |
| vg0517888255 (J) | chr05 | 17888255 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os05g30820.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g30820.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.988; most accessible tissue: Zhenshan97 flower, score: 82.359 |
| vg0517888472 (J) | chr05 | 17888472 | A | C | 64.60% | 0.00% | C -> A |
mr1044 (All); LR P-value: 1.53E-06;
mr1044 (Ind_All); LR P-value: 2.71E-06; mr1069 (All); LR P-value: 3.52E-12; mr1133 (All); LR P-value: 1.04E-18; mr1202 (All); LR P-value: 2.31E-29; mr1482 (Ind_All); LR P-value: 9.07E-06; mr1667 (All); LR P-value: 1.02E-11; mr1827 (All); LR P-value: 2.86E-08; mr1842 (All); LR P-value: 1.13E-17; mr1902 (All); LR P-value: 3.19E-13; mr1002_2 (Ind_All); LR P-value: 9.67E-06; mr1072_2 (All); LR P-value: 8.92E-38; mr1654_2 (All); LR P-value: 6.66E-07 |
LOC_Os05g30830.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.694; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
| vg0517888724 (J) | chr05 | 17888724 | G | A | 65.20% | 0.11% | A -> G |
mr1069 (All); LR P-value: 3.52E-12;
mr1075 (All); LR P-value: 1.84E-28; mr1133 (All); LR P-value: 3.02E-19; mr1202 (All); LR P-value: 1.48E-29; mr1842 (All); LR P-value: 3.66E-16; mr1902 (All); LR P-value: 4.19E-12; mr1072_2 (All); LR P-value: 9.52E-38; mr1654_2 (All); LR P-value: 6.78E-08; mr1756_2 (All); LR P-value: 7.26E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g30820.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.726; most accessible tissue: Zhenshan97 panicle, score: 94.740 |
| vg0517888926 (J) | chr05 | 17888926 | TGGA | T | 96.00% | 0.00% | TGGA -> T,TGGAGGAG GA,TGGAGGA | NA |
LOC_Os05g30820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g30820.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TGGAGGAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TGGAGGAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TGGAGGAGGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.1 Alt: TGGAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30820.2 Alt: TGGAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g30830.1 Alt: TGGAGGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.100; most accessible tissue: Zhenshan97 panicle, score: 96.294 |
| STR0517885732 (J) | chr05 | 17885732 | AAA | AA | 55.30% | 0.00% | AA -> AAA | NA |
|