26 variations found. LOC_Os11g01260 (expressed protein), ranging from 141,219 bp to 142,664 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100141249 (J) | chr11 | 141249 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os11g01260.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.833; most accessible tissue: Callus, score: 88.234 |
| vg1100141257 (J) | chr11 | 141257 | GGGA | G | 99.90% | 0.00% | GGGA -> GGGAGGA,G | NA |
LOC_Os11g01260.1 Alt: GGGAGGA| disruptive_inframe_insertion MODERATE(snpEff)
LOC_Os11g01250.1 Alt: GGGAGGA| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: GGGAGGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: GGGAGGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff) LOC_Os11g01250.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.874; most accessible tissue: Callus, score: 88.234 |
| vg1100141300 (J) | chr11 | 141300 | A | C | 52.20% | 0.19% | C -> A |
mr1598 (All); LR P-value: 5.89E-19;
mr1609 (All); LR P-value: 3.85E-12; mr1889 (Ind_All); LR P-value: 4.62E-10; mr1896 (Ind_All); LR P-value: 4.07E-08; mr1903 (Ind_All); LR P-value: 1.10E-08; mr1907 (Ind_All); LR P-value: 2.01E-14; mr1934 (Ind_All); LR P-value: 2.43E-10; mr1935 (Ind_All); LR P-value: 4.31E-09; mr1835_2 (All); LR P-value: 5.69E-09; mr1836_2 (All); LR P-value: 6.21E-16; mr1889_2 (Ind_All); LR P-value: 3.73E-13; mr1896_2 (Ind_All); LR P-value: 1.49E-07; mr1907_2 (Ind_All); LR P-value: 1.88E-13; mr1934_2 (Ind_All); LR P-value: 4.23E-10 |
LOC_Os11g01260.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g01260.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 67.811; most accessible tissue: Callus, score: 88.234 |
| vg1100141319 (J) | chr11 | 141319 | T | G | 52.20% | 0.04% | G -> T |
mr1598 (All); LR P-value: 7.61E-19;
mr1609 (All); LR P-value: 2.74E-12; mr1889 (Ind_All); LR P-value: 1.03E-10; mr1896 (Ind_All); LR P-value: 1.09E-08; mr1903 (Ind_All); LR P-value: 2.31E-09; mr1907 (Ind_All); LR P-value: 4.48E-15; mr1934 (Ind_All); LR P-value: 8.57E-11; mr1935 (Ind_All); LR P-value: 7.50E-10; mr1332_2 (Ind_All); LR P-value: 8.30E-06; mr1835_2 (All); LR P-value: 8.83E-09; mr1836_2 (All); LR P-value: 6.02E-16; mr1889_2 (Ind_All); LR P-value: 3.16E-13; mr1896_2 (Ind_All); LR P-value: 8.98E-08; mr1907_2 (Ind_All); LR P-value: 8.84E-14; mr1934_2 (Ind_All); LR P-value: 1.93E-10 |
LOC_Os11g01260.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 67.898; most accessible tissue: Callus, score: 88.234 |
| vg1100141349 (J) | chr11 | 141349 | A | AGCCCTC GCTACGC CTTCG | 99.60% | 0.00% | A -> AGCCCTCGCT ACGCCTTCGA CGACTCC,AG CCCTCGCT,A GCCCTCGCTA CGCCTTCG,A GCCCTCGCTA CGCCTTCGAC GACTCCAGT, AGCCCTCGCT ACGCCTTCGA CG,AGCCCTC GCTACGCCTT CGACGACTCC AGTAAGCCC | NA |
LOC_Os11g01250.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCC| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCC| intron_variant MODIFIER(snpEff) LOC_Os11g01250.1 Alt: AGCCCTCGCTACGCCTTCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AGCCCTCGCTACGCCTTCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCTACGCCTTCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCTACGCCTTCG| intron_variant MODIFIER(snpEff) LOC_Os11g01250.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGTAAGCCC| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGTAAGCCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGTAAGCCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGTAAGCCC| intron_variant MODIFIER(snpEff) LOC_Os11g01250.1 Alt: AGCCCTCGCT| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AGCCCTCGCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCT| intron_variant MODIFIER(snpEff) LOC_Os11g01250.1 Alt: AGCCCTCGCTACGCCTTCGACG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AGCCCTCGCTACGCCTTCGACG| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCTACGCCTTCGACG| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCTACGCCTTCGACG| intron_variant MODIFIER(snpEff) LOC_Os11g01250.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGT| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: AGCCCTCGCTACGCCTTCGACGACTCCAGT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.635; most accessible tissue: Zhenshan97 flower, score: 87.671 |
| vg1100141400 (J) | chr11 | 141400 | A | G | 96.70% | 0.00% | A -> G | NA |
LOC_Os11g01250.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.130; most accessible tissue: Zhenshan97 flower, score: 87.040 |
| vg1100141408 (J) | chr11 | 141408 | A | G | 52.20% | 0.11% | G -> A |
mr1032 (Ind_All); LR P-value: 7.79E-06;
mr1478 (Ind_All); LR P-value: 7.89E-06; mr1609 (All); LR P-value: 8.92E-12; mr1889 (Ind_All); LR P-value: 2.11E-10; mr1903 (Ind_All); LR P-value: 1.89E-08; mr1907 (Ind_All); LR P-value: 3.22E-14; mr1934 (Ind_All); LR P-value: 1.03E-09; mr1935 (Ind_All); LR P-value: 1.19E-08; mr1835_2 (All); LR P-value: 4.37E-09; mr1889_2 (Ind_All); LR P-value: 8.99E-14; mr1896_2 (Ind_All); LR P-value: 6.26E-08; mr1907_2 (Ind_All); LR P-value: 3.24E-13; mr1934_2 (Ind_All); LR P-value: 5.61E-10 |
LOC_Os11g01250.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 |
| vg1100141411 (J) | chr11 | 141411 | G | A | 98.10% | 1.52% | G -> A | NA |
LOC_Os11g01250.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 |
| vg1100141415 (J) | chr11 | 141415 | CTG | C | 98.10% | 0.00% | CTG -> C | NA |
LOC_Os11g01250.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.973; most accessible tissue: Zhenshan97 flower, score: 87.172 |
| vg1100141429 (J) | chr11 | 141429 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.926; most accessible tissue: Callus, score: 90.654 |
| vg1100141468 (J) | chr11 | 141468 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os11g01250.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.180; most accessible tissue: Callus, score: 90.654 |
| vg1100141481 (J) | chr11 | 141481 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.686; most accessible tissue: Callus, score: 90.654 |
| vg1100141539 (J) | chr11 | 141539 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.268; most accessible tissue: Callus, score: 90.654 |
| vg1100141578 (J) | chr11 | 141578 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.274; most accessible tissue: Zhenshan97 flower, score: 71.992 |
| vg1100141579 (J) | chr11 | 141579 | T | C | 55.80% | 0.08% | C -> T |
mr1609 (All); LR P-value: 6.59E-11;
mr1835 (All); LR P-value: 2.57E-06; mr1889 (Ind_All); LR P-value: 7.18E-10; mr1903 (Ind_All); LR P-value: 1.71E-08; mr1904 (All); LR P-value: 3.58E-10; mr1907 (Ind_All); LR P-value: 3.29E-14; mr1934 (Ind_All); LR P-value: 3.42E-10; mr1935 (Ind_All); LR P-value: 6.99E-09; mr1889_2 (Ind_All); LR P-value: 4.39E-13; mr1896_2 (Ind_All); LR P-value: 1.78E-07; mr1907_2 (Ind_All); LR P-value: 2.54E-13; mr1934_2 (Ind_All); LR P-value: 5.56E-10 |
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 56.229; most accessible tissue: Zhenshan97 flower, score: 71.992 |
| vg1100141615 (J) | chr11 | 141615 | C | T | 56.30% | 0.04% | T -> C |
mr1032 (Ind_All); LR P-value: 3.72E-06;
mr1609 (All); LR P-value: 2.24E-11; mr1835 (All); LR P-value: 2.31E-06; mr1889 (Ind_All); LR P-value: 1.20E-10; mr1896 (Ind_All); LR P-value: 1.31E-08; mr1903 (Ind_All); LR P-value: 3.81E-09; mr1904 (All); LR P-value: 5.58E-11; mr1907 (Ind_All); LR P-value: 1.17E-14; mr1934 (Ind_All); LR P-value: 3.85E-11; mr1935 (Ind_All); LR P-value: 2.92E-09; mr1332_2 (Ind_All); LR P-value: 4.01E-06; mr1383_2 (Ind_All); LR P-value: 2.25E-07; mr1520_2 (All); LR P-value: 2.50E-11; mr1835_2 (All); LR P-value: 3.03E-09; mr1889_2 (Ind_All); LR P-value: 9.44E-15; mr1896_2 (Ind_All); LR P-value: 5.99E-09; mr1904_2 (All); LR P-value: 4.93E-13; mr1907_2 (Ind_All); LR P-value: 1.00E-14; mr1934_2 (Ind_All); LR P-value: 4.83E-11 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g01250.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.827; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg1100141645 (J) | chr11 | 141645 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os11g01250.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g01240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.790; most accessible tissue: Zhenshan97 flower, score: 69.775 |
| vg1100141854 (J) | chr11 | 141854 | C | T | 55.90% | 0.21% | T -> C |
mr1032 (Ind_All); LR P-value: 5.04E-06;
mr1478 (All); LR P-value: 1.20E-13; mr1478 (Ind_All); LR P-value: 5.37E-06; mr1609 (All); LR P-value: 8.74E-12; mr1835 (All); LR P-value: 6.55E-07; mr1889 (Ind_All); LR P-value: 4.10E-12; mr1896 (Ind_All); LR P-value: 7.06E-10; mr1903 (Ind_All); LR P-value: 2.67E-10; mr1904 (All); LR P-value: 5.82E-11; mr1907 (Ind_All); LR P-value: 8.33E-16; mr1934 (Ind_All); LR P-value: 1.95E-11; mr1935 (Ind_All); LR P-value: 6.79E-10; mr1332_2 (Ind_All); LR P-value: 1.24E-06; mr1520_2 (All); LR P-value: 3.11E-11; mr1835_2 (All); LR P-value: 2.85E-09; mr1889_2 (Ind_All); LMM P-value: 3.76E-06; LR P-value: 1.29E-15; mr1896_2 (Ind_All); LR P-value: 1.29E-09; mr1904_2 (All); LR P-value: 9.97E-13; mr1907_2 (Ind_All); LR P-value: 9.62E-15; mr1934_2 (Ind_All); LR P-value: 7.40E-12 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g01250.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 |
| vg1100142045 (J) | chr11 | 142045 | G | GAA | 52.10% | 0.08% | GAA -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g01250.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g01260.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.384; most accessible tissue: Callus, score: 62.452 |
| vg1100142217 (J) | chr11 | 142217 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os11g01250.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 50.826; most accessible tissue: Callus, score: 78.814 |
| vg1100142231 (J) | chr11 | 142231 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os11g01250.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g01240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01260.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.264; most accessible tissue: Callus, score: 78.814 |
| vg1100142572 (J) | chr11 | 142572 | A | ATGCGAG GACTAGT CGTT | 56.00% | 0.00% | ATGCGAGGAC TAGTCGTT -> A | NA |
LOC_Os11g01260.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.305; most accessible tissue: Callus, score: 93.380 |
| vg1100142621 (J) | chr11 | 142621 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os11g01260.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g01250.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.469; most accessible tissue: Minghui63 flower, score: 92.540 |
| vg1100142630 (J) | chr11 | 142630 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os11g01260.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os11g01250.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.982; most accessible tissue: Minghui63 flower, score: 92.509 |
| vg1100142655 (J) | chr11 | 142655 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os11g01260.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os11g01250.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.333; most accessible tissue: Minghui63 flower, score: 92.509 |
| vg1100142659 (J) | chr11 | 142659 | A | AATTGTG ATGGTGC C | 99.90% | 0.00% | A -> AATTGTGATG GTGCC | NA |
LOC_Os11g01260.1 Alt: AATTGTGATGGTGCC| frameshift_variant&stop_lost&splice_region_variant HIGH(snpEff)
LOC_Os11g01250.1 Alt: AATTGTGATGGTGCC| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g01240.1 Alt: AATTGTGATGGTGCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g01270.1 Alt: AATTGTGATGGTGCC| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.697; most accessible tissue: Minghui63 flower, score: 92.477 |