19 variations found. LOC_Os05g01635 (expressed protein), ranging from 375,944 bp to 378,250 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0500376103 (J) | chr05 | 376103 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os05g01635.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g01630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376139 (J) | chr05 | 376139 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os05g01635.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g01630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376319 (J) | chr05 | 376319 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os05g01635.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g01630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376514 (J) | chr05 | 376514 | ACT | A | 86.60% | 0.00% | ACT -> A | NA |
LOC_Os05g01635.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376518 (J) | chr05 | 376518 | A | C | 65.60% | 0.00% | C -> A |
mr1105 (All); LR P-value: 1.48E-35;
mr1201 (Ind_All); LR P-value: 6.76E-08; mr1219 (Ind_All); LR P-value: 1.29E-07; mr1274 (Ind_All); LR P-value: 6.05E-08; mr1445 (All); LR P-value: 3.33E-06; mr1506 (All); LR P-value: 7.86E-08; mr1529 (All); LR P-value: 1.07E-17; mr1557 (All); LR P-value: 1.23E-17; mr1636 (All); LR P-value: 1.35E-11; mr1641 (All); LR P-value: 3.96E-13; mr1683 (All); LR P-value: 3.04E-11; mr1715 (All); LR P-value: 4.56E-19; mr1776 (All); LR P-value: 8.15E-09; mr1838 (All); LR P-value: 2.51E-21; mr1839 (All); LR P-value: 2.00E-24; mr1909 (All); LR P-value: 3.12E-14; mr1105_2 (All); LR P-value: 9.07E-33; mr1201_2 (Ind_All); LR P-value: 5.00E-09; mr1219_2 (Ind_All); LR P-value: 8.98E-09; mr1274_2 (Ind_All); LR P-value: 2.72E-07; mr1334_2 (Ind_All); LR P-value: 4.46E-07; mr1557_2 (All); LR P-value: 4.84E-17; mr1636_2 (All); LR P-value: 7.45E-13; mr1641_2 (All); LR P-value: 1.95E-13; mr1659_2 (All); LR P-value: 8.51E-08; mr1683_2 (All); LR P-value: 2.49E-07; mr1767_2 (All); LR P-value: 1.85E-16; mr1838_2 (All); LR P-value: 1.41E-13; mr1909_2 (All); LR P-value: 1.42E-07; mr1921_2 (All); LR P-value: 8.64E-08 |
LOC_Os05g01635.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376735 (J) | chr05 | 376735 | C | T | 65.70% | 0.02% | T -> C |
mr1105 (All); LR P-value: 2.17E-35;
mr1201 (Ind_All); LR P-value: 6.76E-08; mr1219 (Ind_All); LR P-value: 1.29E-07; mr1274 (Ind_All); LR P-value: 6.05E-08; mr1445 (All); LR P-value: 3.12E-06; mr1506 (All); LR P-value: 7.77E-08; mr1557 (All); LR P-value: 1.37E-17; mr1636 (All); LR P-value: 1.12E-11; mr1641 (All); LR P-value: 4.11E-13; mr1683 (All); LR P-value: 1.71E-11; mr1715 (All); LR P-value: 3.66E-19; mr1776 (All); LR P-value: 7.85E-09; mr1838 (All); LR P-value: 3.13E-21; mr1839 (All); LR P-value: 3.04E-24; mr1909 (All); LR P-value: 3.70E-14; mr1944 (All); LR P-value: 9.04E-34; mr1105_2 (All); LR P-value: 5.88E-33; mr1201_2 (Ind_All); LR P-value: 5.00E-09; mr1219_2 (Ind_All); LR P-value: 8.98E-09; mr1274_2 (Ind_All); LR P-value: 2.72E-07; mr1334_2 (Ind_All); LR P-value: 4.46E-07; mr1557_2 (All); LR P-value: 1.80E-17; mr1636_2 (All); LR P-value: 8.18E-13; mr1641_2 (All); LR P-value: 2.04E-13; mr1659_2 (All); LR P-value: 8.02E-08; mr1683_2 (All); LR P-value: 2.31E-07; mr1767_2 (All); LR P-value: 1.26E-16; mr1838_2 (All); LR P-value: 1.01E-13; mr1909_2 (All); LR P-value: 1.75E-07; mr1921_2 (All); LR P-value: 1.05E-07; mr1968_2 (All); LR P-value: 1.14E-20 |
LOC_Os05g01635.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g01635.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376792 (J) | chr05 | 376792 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os05g01635.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500376864 (J) | chr05 | 376864 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os05g01635.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g01630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377022 (J) | chr05 | 377022 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os05g01635.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os05g01630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g01630.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377042 (J) | chr05 | 377042 | G | C | 99.00% | 0.00% | G -> C | NA |
LOC_Os05g01635.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377108 (J) | chr05 | 377108 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os05g01630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g01640.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01630.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g01635.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377242 (J) | chr05 | 377242 | G | A | 97.20% | 0.00% | G -> A | NA |
LOC_Os05g01635.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377427 (J) | chr05 | 377427 | A | G | 62.80% | 0.00% | G -> A |
mr1201 (Ind_All); LR P-value: 8.64E-07;
mr1638 (All); LR P-value: 7.83E-28; mr1198_2 (All); LR P-value: 9.43E-09; mr1201_2 (Ind_All); LR P-value: 8.90E-07; mr1219_2 (Ind_All); LR P-value: 7.33E-07; mr1405_2 (All); LR P-value: 5.95E-06; mr1575_2 (All); LR P-value: 8.67E-14; mr1636_2 (All); LR P-value: 6.06E-12; mr1641_2 (All); LR P-value: 4.26E-12; mr1659_2 (All); LR P-value: 2.27E-08; mr1767_2 (All); LR P-value: 9.52E-15; mr1838_2 (All); LR P-value: 1.16E-13; mr1921_2 (All); LR P-value: 2.53E-07; mr1968_2 (All); LR P-value: 1.65E-20 |
LOC_Os05g01635.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377686 (J) | chr05 | 377686 | A | G | 62.80% | 0.00% | G -> A |
mr1201 (Ind_All); LR P-value: 8.64E-07;
mr1638 (All); LR P-value: 6.71E-28; mr1198_2 (All); LR P-value: 9.92E-09; mr1201_2 (Ind_All); LR P-value: 8.90E-07; mr1219_2 (Ind_All); LR P-value: 7.33E-07; mr1405_2 (All); LR P-value: 5.82E-06; mr1575_2 (All); LR P-value: 7.47E-14; mr1636_2 (All); LR P-value: 5.53E-12; mr1641_2 (All); LR P-value: 3.95E-12; mr1659_2 (All); LR P-value: 2.23E-08; mr1767_2 (All); LR P-value: 1.01E-14; mr1838_2 (All); LR P-value: 1.22E-13; mr1921_2 (All); LR P-value: 2.28E-07; mr1968_2 (All); LR P-value: 1.97E-20 |
LOC_Os05g01635.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377935 (J) | chr05 | 377935 | G | A | 65.70% | 0.00% | A -> G |
mr1105 (All); LR P-value: 3.46E-35;
mr1116 (All); LR P-value: 2.46E-16; mr1201 (Ind_All); LR P-value: 6.76E-08; mr1219 (Ind_All); LR P-value: 1.29E-07; mr1274 (Ind_All); LR P-value: 6.05E-08; mr1445 (All); LR P-value: 1.19E-06; mr1506 (All); LR P-value: 3.12E-08; mr1529 (All); LR P-value: 1.79E-18; mr1557 (All); LR P-value: 2.02E-18; mr1636 (All); LR P-value: 1.41E-12; mr1641 (All); LR P-value: 4.74E-14; mr1683 (All); LR P-value: 4.95E-12; mr1715 (All); LR P-value: 1.37E-18; mr1776 (All); LR P-value: 2.42E-09; mr1779 (All); LR P-value: 5.71E-07; mr1838 (All); LR P-value: 1.60E-21; mr1839 (All); LR P-value: 3.83E-24; mr1909 (All); LR P-value: 6.36E-15; mr1944 (All); LR P-value: 1.27E-33; mr1105_2 (All); LR P-value: 6.55E-32; mr1201_2 (Ind_All); LR P-value: 5.00E-09; mr1219_2 (Ind_All); LR P-value: 8.98E-09; mr1274_2 (Ind_All); LR P-value: 2.72E-07; mr1334_2 (Ind_All); LR P-value: 4.46E-07; mr1557_2 (All); LR P-value: 8.20E-17; mr1636_2 (All); LR P-value: 1.47E-12; mr1641_2 (All); LR P-value: 3.00E-13; mr1659_2 (All); LR P-value: 7.11E-08; mr1683_2 (All); LR P-value: 2.33E-07; mr1767_2 (All); LR P-value: 4.60E-16; mr1838_2 (All); LR P-value: 1.91E-13; mr1921_2 (All); LR P-value: 1.27E-07 |
LOC_Os05g01635.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500377955 (J) | chr05 | 377955 | G | A | 96.70% | 0.00% | G -> A | NA |
LOC_Os05g01635.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500378036 (J) | chr05 | 378036 | G | GGTGGGA | 63.50% | 0.00% | GGTGGGA -> G | NA |
LOC_Os05g01635.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500378042 (J) | chr05 | 378042 | A | C | 98.30% | 0.00% | A -> C |
mr1105 (All); LR P-value: 2.16E-35;
mr1201 (Ind_All); LR P-value: 4.21E-07; mr1219 (Ind_All); LR P-value: 5.98E-07; mr1274 (Ind_All); LR P-value: 6.46E-07; mr1445 (All); LR P-value: 5.82E-06; mr1506 (All); LR P-value: 8.05E-08; mr1529 (All); LR P-value: 1.40E-17; mr1557 (All); LR P-value: 3.27E-17; mr1636 (All); LR P-value: 8.73E-12; mr1641 (All); LR P-value: 5.58E-13; mr1683 (All); LR P-value: 8.61E-11; mr1715 (All); LR P-value: 1.55E-18; mr1776 (All); LR P-value: 1.33E-08; mr1779 (All); LR P-value: 3.96E-07; mr1838 (All); LR P-value: 2.30E-21; mr1839 (All); LR P-value: 4.37E-24; mr1909 (All); LR P-value: 3.70E-14; mr1944 (All); LR P-value: 1.27E-33; mr1105_2 (All); LR P-value: 1.04E-32; mr1201_2 (Ind_All); LR P-value: 6.80E-08; mr1219_2 (Ind_All); LR P-value: 1.58E-07; mr1274_2 (Ind_All); LR P-value: 5.50E-07; mr1557_2 (All); LR P-value: 4.84E-17; mr1636_2 (All); LR P-value: 3.29E-13; mr1641_2 (All); LR P-value: 1.11E-13; mr1659_2 (All); LR P-value: 9.64E-08; mr1683_2 (All); LR P-value: 1.19E-07; mr1767_2 (All); LR P-value: 2.82E-16; mr1838_2 (All); LR P-value: 2.46E-13; mr1909_2 (All); LR P-value: 1.36E-07; mr1921_2 (All); LR P-value: 5.16E-08 |
LOC_Os05g01635.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0500378083 (J) | chr05 | 378083 | G | A | 97.20% | 0.00% | G -> A | NA |
LOC_Os05g01635.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |