12 variations found. LOC_Os08g34240 (CAMK_KIN1%2FSNF1%2FNim1_like.33 - CAMK includes calcium%2Fcalmodulin depedent protein kinases; expressed), ranging from 21,466,750 bp to 21,468,619 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0821466817 (J) | chr08 | 21466817 | ACGACGC CGC | A | 55.90% | 0.02% | A -> ACGACGCCGC ,ACGACGC,A CGACGCCGCC GACGC | NA |
LOC_Os08g34240.1 Alt: ACGACGCCGCCGACGC| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g34240.1 Alt: ACGACGC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g34240.1 Alt: ACGACGCCGC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.202; most accessible tissue: Minghui63 young leaf, score: 99.683 |
| vg0821466980 (J) | chr08 | 21466980 | G | A | 89.60% | 0.00% | G -> A | NA |
LOC_Os08g34240.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.922; most accessible tissue: Minghui63 flag leaf, score: 98.736 |
| vg0821466997 (J) | chr08 | 21466997 | TGAG | T | 75.20% | 0.00% | T -> TGAG,TGAGG AG | NA |
N Alt: TGAGGAG/silent_mutation(CooVar)
LOC_Os08g34240.1 Alt: TGAG| start_lost&disruptive_inframe_insertion HIGH(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.862; most accessible tissue: Minghui63 flag leaf, score: 98.748 |
| vg0821467030 (J) | chr08 | 21467030 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os08g34240.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.864; most accessible tissue: Minghui63 flag leaf, score: 98.834 |
| vg0821467062 (J) | chr08 | 21467062 | G | A | 78.10% | 0.00% | A -> G |
Grain_thickness (All); LR P-value: 5.78E-36;
mr1533 (All); LR P-value: 2.90E-36; mr1668 (Jap_All); LR P-value: 5.70E-07; mr1980 (All); LR P-value: 2.95E-32; mr1410_2 (All); LR P-value: 1.65E-13; mr1533_2 (All); LR P-value: 1.21E-40; mr1742_2 (Jap_All); LR P-value: 4.14E-09; mr1952_2 (Jap_All); LR P-value: 6.01E-08; mr1980_2 (All); LR P-value: 1.25E-18 |
LOC_Os08g34240.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.779; most accessible tissue: Minghui63 flag leaf, score: 98.850 |
| vg0821467196 (J) | chr08 | 21467196 | C | T | 89.90% | 0.00% | C -> T |
mr1016 (Jap_All); LR P-value: 8.43E-10;
mr1017 (Jap_All); LR P-value: 8.69E-11; mr1132 (Jap_All); LR P-value: 5.48E-11; mr1178 (Jap_All); LR P-value: 3.60E-10; mr1248 (All); LR P-value: 7.96E-07; mr1301 (All); LR P-value: 4.08E-20; mr1364 (Jap_All); LR P-value: 6.16E-07; mr1388 (All); LR P-value: 2.16E-06; mr1410 (All); LR P-value: 1.35E-14; mr1443 (Jap_All); LR P-value: 6.26E-07; mr1510 (All); LR P-value: 2.01E-07; mr1533 (Jap_All); LR P-value: 1.05E-10; mr1551 (Jap_All); LR P-value: 2.79E-07; mr1554 (All); LR P-value: 4.11E-08; mr1602 (All); LR P-value: 2.05E-06; mr1668 (All); LR P-value: 5.71E-08; mr1699 (All); LR P-value: 6.64E-35; mr1871 (All); LR P-value: 4.85E-16; mr1871 (Jap_All); LR P-value: 4.37E-06; mr1980 (Jap_All); LR P-value: 1.04E-12; mr1042_2 (All); LR P-value: 6.11E-21; mr1178_2 (Jap_All); LR P-value: 2.67E-13; mr1206_2 (All); LR P-value: 6.85E-06; mr1533_2 (Jap_All); LR P-value: 4.16E-11; mr1668_2 (All); LR P-value: 5.90E-08; mr1696_2 (All); LR P-value: 5.90E-07; mr1699_2 (All); LR P-value: 8.52E-34; mr1705_2 (All); LR P-value: 2.83E-09; mr1742_2 (All); LR P-value: 1.72E-14; mr1769_2 (All); LR P-value: 1.44E-10; mr1871_2 (All); LR P-value: 2.49E-23 |
LOC_Os08g34240.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.369; most accessible tissue: Minghui63 flag leaf, score: 98.899 |
| vg0821467912 (J) | chr08 | 21467912 | C | T | 89.60% | 0.00% | C -> T | NA |
LOC_Os08g34240.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.916; most accessible tissue: Minghui63 flag leaf, score: 98.970 |
| vg0821468340 (J) | chr08 | 21468340 | G | A | 89.90% | 0.00% | G -> A |
mr1016 (Jap_All); LR P-value: 8.43E-10;
mr1017 (Jap_All); LR P-value: 8.69E-11; mr1132 (Jap_All); LR P-value: 5.48E-11; mr1178 (Jap_All); LR P-value: 3.60E-10; mr1248 (All); LR P-value: 1.37E-06; mr1301 (All); LR P-value: 7.26E-19; mr1364 (Jap_All); LR P-value: 6.16E-07; mr1410 (All); LR P-value: 1.09E-13; mr1443 (Jap_All); LR P-value: 6.26E-07; mr1510 (All); LR P-value: 1.28E-06; mr1533 (Jap_All); LR P-value: 1.05E-10; mr1551 (Jap_All); LR P-value: 2.79E-07; mr1554 (All); LR P-value: 2.04E-07; mr1602 (All); LR P-value: 6.15E-06; mr1668 (All); LR P-value: 1.96E-07; mr1699 (All); LR P-value: 9.32E-35; mr1871 (All); LR P-value: 1.70E-15; mr1871 (Jap_All); LR P-value: 4.37E-06; mr1980 (Jap_All); LR P-value: 1.04E-12; mr1042_2 (All); LR P-value: 2.00E-19; mr1178_2 (Jap_All); LR P-value: 2.67E-13; mr1206_2 (All); LR P-value: 8.56E-06; mr1533_2 (Jap_All); LR P-value: 4.16E-11; mr1582_2 (All); LR P-value: 2.86E-07; mr1668_2 (All); LR P-value: 1.11E-07; mr1699_2 (All); LR P-value: 1.78E-32; mr1742_2 (All); LR P-value: 1.49E-13; mr1769_2 (All); LR P-value: 1.64E-09; mr1871_2 (All); LR P-value: 5.46E-22 |
LOC_Os08g34240.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.714; most accessible tissue: Minghui63 flag leaf, score: 98.873 |
| vg0821468433 (J) | chr08 | 21468433 | C | T | 77.80% | 0.00% | T -> C |
Grain_thickness (All); LR P-value: 2.60E-35;
mr1308 (All); LR P-value: 3.01E-17; mr1308 (Jap_All); LR P-value: 1.32E-06; mr1364 (All); LR P-value: 1.77E-07; mr1401 (All); LR P-value: 3.10E-15; mr1410 (Jap_All); LR P-value: 1.16E-11; mr1443 (All); LR P-value: 8.48E-07; mr1533 (All); LR P-value: 1.24E-36; mr1533 (Jap_All); LR P-value: 1.62E-08; mr1622 (All); LR P-value: 2.52E-06; mr1668 (Jap_All); LR P-value: 1.57E-06; mr1980 (All); LR P-value: 6.24E-33; mr1410_2 (Jap_All); LR P-value: 1.04E-11; mr1533_2 (All); LR P-value: 1.50E-37; mr1699_2 (Jap_All); LR P-value: 8.22E-17; mr1742_2 (Jap_All); LR P-value: 3.92E-09; mr1746_2 (All); LR P-value: 9.28E-17 |
LOC_Os08g34240.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.374; most accessible tissue: Minghui63 flower, score: 98.672 |
| vg0821468535 (J) | chr08 | 21468535 | A | AT | 77.90% | 0.00% | AT -> A | NA |
LOC_Os08g34240.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.366; most accessible tissue: Minghui63 flower, score: 98.763 |
| vg0821468556 (J) | chr08 | 21468556 | A | G | 78.00% | 0.00% | G -> A |
Grain_thickness (All); LR P-value: 6.43E-36;
mr1308 (All); LR P-value: 1.40E-17; mr1308 (Jap_All); LR P-value: 1.32E-06; mr1364 (All); LR P-value: 1.16E-07; mr1410 (All); LR P-value: 1.13E-13; mr1410 (Jap_All); LR P-value: 1.16E-11; mr1443 (All); LR P-value: 6.27E-07; mr1533 (All); LR P-value: 3.20E-37; mr1533 (Jap_All); LR P-value: 1.62E-08; mr1668 (Jap_All); LR P-value: 1.57E-06; mr1806 (All); LR P-value: 4.06E-08; mr1980 (All); LR P-value: 1.71E-33; mr1410_2 (All); LR P-value: 8.37E-14; mr1410_2 (Jap_All); LR P-value: 1.04E-11; mr1533_2 (All); LR P-value: 1.59E-39; mr1699_2 (Jap_All); LR P-value: 8.22E-17; mr1742_2 (Jap_All); LR P-value: 3.92E-09; mr1980_2 (All); LR P-value: 6.33E-18 |
LOC_Os08g34240.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.274; most accessible tissue: Minghui63 flower, score: 98.731 |
| STR0821466818 (J) | chr08 | 21466818 | CGACGCC GACGCCG ACGCCG | CGACGCC GACGCCG | 69.30% | 0.00% | CGACGCCGAC GCCG -> CGACGCCGAC GCCGACGCCG | NA |
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