19 variations found. LOC_Os05g39260 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 23,020,499 bp to 23,021,809 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0523020765 (J) | chr05 | 23020765 | T | C | 62.70% | 0.00% | C -> T |
mr1027 (All); LR P-value: 1.01E-65;
mr1064 (All); LR P-value: 5.13E-37; mr1125 (All); LR P-value: 6.54E-49; mr1448 (All); LR P-value: 5.25E-32; mr1534 (All); LR P-value: 5.04E-41; mr1594 (All); LR P-value: 1.96E-56; mr1718 (All); LR P-value: 1.98E-89; mr1795 (All); LR P-value: 3.47E-53; mr1890 (All); LR P-value: 1.39E-39; mr1064_2 (All); LR P-value: 2.79E-60; mr1125_2 (All); LR P-value: 2.12E-63; mr1181_2 (All); LR P-value: 2.28E-34; mr1246_2 (All); LR P-value: 3.77E-75; mr1316_2 (All); LR P-value: 3.53E-23; mr1377_2 (All); LR P-value: 8.05E-12; mr1551_2 (All); LR P-value: 1.51E-21; mr1609_2 (All); LR P-value: 4.07E-23; mr1689_2 (All); LR P-value: 3.46E-36; mr1718_2 (All); LR P-value: 1.14E-116; mr1721_2 (All); LR P-value: 3.23E-48; mr1733_2 (All); LR P-value: 1.67E-61; mr1841_2 (All); LR P-value: 7.32E-32; mr1888_2 (All); LR P-value: 6.76E-36; mr1938_2 (All); LR P-value: 2.08E-14 |
LOC_Os05g39260.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.619; most accessible tissue: Zhenshan97 young leaf, score: 99.422 |
| vg0523020785 (J) | chr05 | 23020785 | T | G | 63.00% | 0.00% | G -> T |
mr1027 (All); LR P-value: 1.44E-65;
mr1064 (All); LR P-value: 2.35E-36; mr1484 (All); LR P-value: 8.95E-16; mr1534 (All); LR P-value: 9.73E-40; mr1718 (All); LR P-value: 3.13E-82; mr1064_2 (All); LR P-value: 1.59E-60; mr1125_2 (All); LR P-value: 1.87E-63; mr1316_2 (All); LR P-value: 5.37E-22; mr1377_2 (All); LR P-value: 1.11E-11; mr1484_2 (All); LR P-value: 1.54E-24; mr1609_2 (All); LR P-value: 5.49E-22; mr1689_2 (All); LR P-value: 1.62E-36; mr1718_2 (All); LR P-value: 2.39E-111; mr1888_2 (All); LR P-value: 1.61E-34; mr1915_2 (All); LR P-value: 2.75E-06; mr1938_2 (All); LR P-value: 6.60E-14 |
LOC_Os05g39260.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.496; most accessible tissue: Zhenshan97 young leaf, score: 99.305 |
| vg0523020840 (J) | chr05 | 23020840 | C | G | 99.70% | 0.00% | C -> G | NA |
LOC_Os05g39260.1 Alt: G| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 89.864; most accessible tissue: Zhenshan97 young leaf, score: 98.897 |
| vg0523021200 (J) | chr05 | 23021200 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os05g39260.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 97.856; most accessible tissue: Zhenshan97 young leaf, score: 99.529 |
| vg0523021346 (J) | chr05 | 23021346 | G | C | 58.90% | 0.00% | C -> G |
mr1498 (Ind_All); LR P-value: 1.78E-09;
mr1889 (Ind_All); LR P-value: 2.85E-11; mr1896 (Ind_All); LR P-value: 5.99E-09; mr1903 (Ind_All); LR P-value: 2.98E-09; mr1907 (Ind_All); LR P-value: 4.98E-14; mr1925 (Ind_All); LR P-value: 9.67E-06; mr1498_2 (Ind_All); LR P-value: 4.46E-08; mr1889_2 (Ind_All); LR P-value: 2.87E-10; mr1896_2 (Ind_All); LR P-value: 3.60E-08; mr1907_2 (Ind_All); LR P-value: 2.19E-09 |
LOC_Os05g39260.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.207; most accessible tissue: Zhenshan97 young leaf, score: 99.457 |
| vg0523021591 (J) | chr05 | 23021591 | A | G | 96.90% | 0.00% | A -> G |
LOC_Os05g39260.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.649; most accessible tissue: Minghui63 root, score: 98.830 |
|
| vg0523021606 (J) | chr05 | 23021606 | C | T | 96.70% | 0.00% | C -> T |
LOC_Os05g39260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.933; most accessible tissue: Minghui63 root, score: 98.615 |
|
| vg0523021660 (J) | chr05 | 23021660 | C | T | 66.10% | 0.00% | T -> C | NA |
LOC_Os05g39260.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.988; most accessible tissue: Minghui63 root, score: 97.994 |
| vg0523021662 (J) | chr05 | 23021662 | A | T | 97.00% | 0.00% | A -> T | NA |
LOC_Os05g39260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.119; most accessible tissue: Minghui63 root, score: 97.983 |
| vg0523021738 (J) | chr05 | 23021738 | TGCTGAT TGCTACA G | T | 99.00% | 0.00% | TGCTGATTGC TACAG -> T | NA |
LOC_Os05g39260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 89.605; most accessible tissue: Minghui63 root, score: 97.367 |
| vg0523021748 (J) | chr05 | 23021748 | A | T | 64.90% | 0.00% | T -> A | NA |
LOC_Os05g39260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.159; most accessible tissue: Minghui63 root, score: 97.311 |
| vg0523021750 (J) | chr05 | 23021750 | C | G | 96.80% | 0.23% | C -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g39260.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.220; most accessible tissue: Minghui63 root, score: 97.311 |
|
| vg0523021766 (J) | chr05 | 23021766 | A | C | 99.80% | 0.00% | A -> C | NA |
LOC_Os05g39260.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 86.720; most accessible tissue: Minghui63 root, score: 96.744 |
| vg0523021769 (J) | chr05 | 23021769 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os05g39260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.906; most accessible tissue: Minghui63 root, score: 96.562 |
| vg0523021772 (J) | chr05 | 23021772 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os05g39260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.139; most accessible tissue: Minghui63 root, score: 96.429 |
| vg0523021773 (J) | chr05 | 23021773 | G | A | 97.00% | 0.00% | G -> A |
LOC_Os05g39260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.139; most accessible tissue: Minghui63 root, score: 96.429 |
|
| vg0523021777 (J) | chr05 | 23021777 | G | A | 96.90% | 0.00% | G -> A |
LOC_Os05g39260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.177; most accessible tissue: Minghui63 root, score: 96.411 |
|
| vg0523021797 (J) | chr05 | 23021797 | C | T | 66.00% | 0.00% | T -> C | NA |
LOC_Os05g39260.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.339; most accessible tissue: Minghui63 root, score: 96.290 |
| vg0523021800 (J) | chr05 | 23021800 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os05g39260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 84.150; most accessible tissue: Minghui63 root, score: 96.280 |