9 variations found. LOC_Os11g04690 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 1,998,789 bp to 1,999,485 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101998790 (J) | chr11 | 1998790 | A | T | 79.50% | 0.00% | A -> T |
mr1593 (Ind_All); LR P-value: 8.00E-07;
mr1607 (All); LR P-value: 2.06E-09; mr1662 (All); LR P-value: 6.13E-07; mr1686 (Ind_All); LR P-value: 1.00E-06; mr1835 (All); LR P-value: 1.10E-08; mr1835 (Ind_All); LR P-value: 7.22E-08; mr1904 (All); LMM P-value: 5.54E-06; LR P-value: 7.62E-17; mr1904 (Ind_All); LMM P-value: 9.12E-09; LR P-value: 4.05E-15; mr1942 (All); LR P-value: 9.40E-08; mr1024_2 (Ind_All); LR P-value: 5.37E-10; mr1072_2 (Ind_All); LR P-value: 2.82E-08; mr1075_2 (Ind_All); LR P-value: 1.55E-08; mr1077_2 (Ind_All); LR P-value: 5.90E-09; mr1078_2 (Ind_All); LR P-value: 3.13E-09; mr1199_2 (Ind_All); LR P-value: 6.26E-06; mr1200_2 (Ind_All); LR P-value: 1.51E-07; mr1265_2 (All); LR P-value: 6.45E-09; mr1265_2 (Ind_All); LR P-value: 3.98E-09; mr1482_2 (All); LR P-value: 2.20E-07; mr1486_2 (Ind_All); LR P-value: 3.66E-07; mr1528_2 (All); LR P-value: 2.46E-11; mr1528_2 (Ind_All); LR P-value: 7.32E-09; mr1558_2 (Ind_All); LR P-value: 1.15E-07; mr1565_2 (Ind_All); LR P-value: 7.29E-12; mr1593_2 (Ind_All); LR P-value: 2.36E-08; mr1598_2 (Ind_All); LR P-value: 9.38E-11; mr1641_2 (Ind_All); LR P-value: 8.98E-06; mr1659_2 (Ind_All); LR P-value: 2.40E-06; mr1735_2 (Ind_All); LR P-value: 6.36E-06; mr1835_2 (All); LR P-value: 3.35E-13; mr1835_2 (Ind_All); LR P-value: 8.70E-10; mr1838_2 (Ind_All); LR P-value: 4.00E-08; mr1904_2 (All); LR P-value: 9.41E-16; mr1904_2 (Ind_All); LR P-value: 5.25E-11 |
LOC_Os11g04690.1 Alt: T| initiator_codon_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.452; most accessible tissue: Zhenshan97 panicle, score: 80.486 |
| vg1101998891 (J) | chr11 | 1998891 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os11g04690.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 64.340; most accessible tissue: Zhenshan97 panicle, score: 79.799 |
| vg1101998893 (J) | chr11 | 1998893 | C | G | 98.50% | 0.00% | C -> G |
LOC_Os11g04690.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 63.529; most accessible tissue: Zhenshan97 panicle, score: 79.071 |
|
| vg1101999007 (J) | chr11 | 1999007 | G | A | 56.50% | 0.00% | G -> A |
mr1030 (All); LR P-value: 7.75E-06;
mr1272 (Ind_All); LR P-value: 1.77E-06; mr1565 (All); LR P-value: 3.22E-09; mr1663 (All); LR P-value: 3.07E-09; mr1686 (Ind_All); LR P-value: 3.46E-07; mr1835 (Ind_All); LR P-value: 1.12E-06; mr1904 (Ind_All); LMM P-value: 4.29E-08; LR P-value: 4.86E-14; mr1024_2 (Ind_All); LR P-value: 4.95E-10; mr1078_2 (Ind_All); LR P-value: 1.00E-08; mr1183_2 (All); LR P-value: 7.73E-20; mr1265_2 (Ind_All); LR P-value: 3.25E-08; mr1302_2 (All); LR P-value: 4.27E-07; mr1486_2 (Ind_All); LR P-value: 2.23E-06; mr1528_2 (Ind_All); LR P-value: 8.32E-08; mr1558_2 (Ind_All); LR P-value: 6.81E-08; mr1565_2 (All); LR P-value: 1.39E-11; mr1565_2 (Ind_All); LR P-value: 2.05E-11; mr1593_2 (Ind_All); LR P-value: 2.30E-08; mr1598_2 (Ind_All); LR P-value: 4.80E-09; mr1604_2 (All); LR P-value: 4.23E-07; mr1641_2 (Ind_All); LR P-value: 7.40E-06; mr1659_2 (All); LR P-value: 4.62E-10; mr1659_2 (Ind_All); LR P-value: 7.43E-07; mr1735_2 (Ind_All); LR P-value: 5.05E-07; mr1824_2 (All); LR P-value: 4.38E-07; mr1835_2 (Ind_All); LR P-value: 2.40E-09; mr1838_2 (All); LR P-value: 3.15E-15; mr1838_2 (Ind_All); LR P-value: 5.38E-08; mr1904_2 (Ind_All); LR P-value: 2.05E-09 |
LOC_Os11g04690.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 66.756; most accessible tissue: Zhenshan97 panicle, score: 79.071 |
| vg1101999096 (J) | chr11 | 1999096 | C | T | 56.50% | 0.32% | C -> T |
mr1030 (All); LR P-value: 9.59E-06;
mr1663 (All); LR P-value: 2.14E-09; mr1686 (Ind_All); LR P-value: 2.93E-07; mr1835 (Ind_All); LR P-value: 1.14E-06; mr1904 (Ind_All); LMM P-value: 3.78E-08; LR P-value: 4.55E-14; mr1024_2 (Ind_All); LR P-value: 4.78E-10; mr1078_2 (Ind_All); LR P-value: 1.04E-08; mr1265_2 (Ind_All); LR P-value: 6.01E-08; mr1302_2 (All); LR P-value: 7.11E-07; mr1486_2 (Ind_All); LR P-value: 2.48E-06; mr1528_2 (Ind_All); LR P-value: 1.31E-07; mr1558_2 (Ind_All); LR P-value: 9.85E-08; mr1565_2 (All); LR P-value: 4.51E-11; mr1565_2 (Ind_All); LR P-value: 1.12E-10; mr1593_2 (Ind_All); LR P-value: 7.38E-08; mr1659_2 (All); LR P-value: 9.12E-10; mr1659_2 (Ind_All); LR P-value: 1.91E-06; mr1735_2 (Ind_All); LR P-value: 1.04E-06; mr1824_2 (All); LR P-value: 8.28E-07; mr1835_2 (Ind_All); LR P-value: 2.21E-09; mr1838_2 (All); LR P-value: 1.12E-14; mr1838_2 (Ind_All); LR P-value: 1.65E-07; mr1904_2 (Ind_All); LR P-value: 1.69E-09 |
LOC_Os11g04690.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04690.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.300; most accessible tissue: Minghui63 panicle, score: 78.920 |
| vg1101999220 (J) | chr11 | 1999220 | G | GC | 99.80% | 0.00% | G -> GC | NA |
LOC_Os11g04690.1 Alt: GC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 68.466; most accessible tissue: Minghui63 panicle, score: 77.956 |
| vg1101999320 (J) | chr11 | 1999320 | C | T | 64.50% | 0.00% | T -> C | NA |
LOC_Os11g04690.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.966; most accessible tissue: Minghui63 root, score: 76.119 |
| vg1101999349 (J) | chr11 | 1999349 | G | A | 54.70% | 0.32% | G -> A |
mr1565 (All); LR P-value: 2.54E-10;
mr1663 (All); LR P-value: 4.54E-10; mr1686 (Ind_All); LR P-value: 4.14E-07; mr1835 (Ind_All); LR P-value: 1.14E-06; mr1904 (All); LMM P-value: 2.15E-06; mr1904 (Ind_All); LMM P-value: 3.73E-08; LR P-value: 3.94E-14; mr1024_2 (Ind_All); LR P-value: 4.39E-10; mr1078_2 (Ind_All); LR P-value: 1.23E-08; mr1265_2 (Ind_All); LR P-value: 2.93E-08; mr1486_2 (Ind_All); LR P-value: 2.73E-06; mr1528_2 (Ind_All); LR P-value: 5.96E-08; mr1558_2 (Ind_All); LR P-value: 1.08E-07; mr1565_2 (All); LR P-value: 1.25E-12; mr1565_2 (Ind_All); LR P-value: 1.07E-10; mr1593_2 (Ind_All); LR P-value: 7.43E-08; mr1659_2 (All); LR P-value: 2.46E-10; mr1659_2 (Ind_All); LR P-value: 2.00E-06; mr1683_2 (All); LR P-value: 1.55E-07; mr1715_2 (All); LR P-value: 1.22E-16; mr1735_2 (Ind_All); LR P-value: 1.07E-06; mr1824_2 (All); LR P-value: 2.72E-07; mr1835_2 (Ind_All); LR P-value: 2.74E-09; mr1838_2 (All); LR P-value: 1.48E-16; mr1838_2 (Ind_All); LR P-value: 1.86E-07; mr1904_2 (Ind_All); LR P-value: 3.48E-09 |
LOC_Os11g04690.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g04690.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 65.203; most accessible tissue: Minghui63 root, score: 76.721 |
| vg1101999370 (J) | chr11 | 1999370 | C | G | 98.20% | 0.00% | C -> G | NA |
LOC_Os11g04690.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.124; most accessible tissue: Minghui63 root, score: 76.425 |