3 variations found. LOC_Os04g19700 (zinc finger family protein; putative; expressed), ranging from 10,996,900 bp to 10,997,209 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0410997056 (J) | chr04 | 10997056 | C | T | 88.30% | 0.00% | C -> T |
mr1047 (Jap_All); LR P-value: 4.12E-06;
mr1121 (Jap_All); LR P-value: 4.14E-07; mr1157 (Jap_All); LR P-value: 7.62E-06; mr1271 (Jap_All); LR P-value: 4.23E-07; mr1301 (All); LR P-value: 1.48E-24; mr1301 (Jap_All); LR P-value: 7.32E-15; mr1410 (All); LR P-value: 3.18E-14; mr1425 (All); LR P-value: 4.77E-06; mr1446 (Jap_All); LR P-value: 4.35E-06; mr1449 (All); LR P-value: 1.04E-13; mr1454 (All); LR P-value: 9.24E-13; mr1471 (Jap_All); LR P-value: 2.14E-06; mr1580 (Jap_All); LR P-value: 5.46E-10; mr1699 (All); LR P-value: 1.18E-32; mr1715 (All); LR P-value: 3.26E-20; mr1732 (All); LR P-value: 1.33E-12; mr1739 (Jap_All); LR P-value: 3.81E-07; mr1864 (All); LR P-value: 4.28E-11; mr1993 (All); LR P-value: 1.13E-06; mr1993 (Jap_All); LR P-value: 3.57E-08; mr1301_2 (All); LMM P-value: 5.94E-06; LR P-value: 7.78E-26; mr1301_2 (Jap_All); LR P-value: 1.45E-17; mr1410_2 (All); LR P-value: 9.88E-15; mr1699_2 (All); LR P-value: 8.27E-31; mr1905_2 (All); LR P-value: 3.44E-09; mr1993_2 (All); LR P-value: 2.92E-12; mr1993_2 (Jap_All); LR P-value: 1.04E-12 |
LOC_Os04g19700.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.224; most accessible tissue: Minghui63 young leaf, score: 93.394 |
| vg0410997084 (J) | chr04 | 10997084 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os04g19700.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.944; most accessible tissue: Minghui63 young leaf, score: 92.217 |
| vg0410997085 (J) | chr04 | 10997085 | G | A | 79.80% | 0.00% | A -> G |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1077 (All); LR P-value: 1.72E-18; mr1090 (Jap_All); LR P-value: 2.17E-06; mr1121 (Jap_All); LR P-value: 3.42E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (Jap_All); LR P-value: 4.91E-07; mr1282 (All); LR P-value: 1.75E-10; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1449 (Jap_All); LR P-value: 3.88E-08; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1650 (All); LR P-value: 2.32E-12; mr1658 (All); LR P-value: 3.64E-09; mr1712 (All); LR P-value: 5.69E-10; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1741 (All); LR P-value: 5.62E-12; mr1771 (All); LR P-value: 1.17E-45; mr1789 (All); LR P-value: 1.13E-32; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1844 (All); LR P-value: 8.20E-13; mr1844 (Jap_All); LR P-value: 6.15E-06; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1926 (All); LR P-value: 5.53E-43; mr1982 (All); LR P-value: 1.30E-13; mr1282_2 (All); LR P-value: 5.06E-10; mr1310_2 (All); LR P-value: 1.20E-31; mr1399_2 (All); LR P-value: 1.08E-07; mr1520_2 (All); LR P-value: 5.55E-12 |
LOC_Os04g19700.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.944; most accessible tissue: Minghui63 young leaf, score: 92.217 |