10 variations found. LOC_Os06g50250 (conserved hypothetical protein), ranging from 30,422,606 bp to 30,423,505 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0630422637 (J) | chr06 | 30422637 | C | T | 51.20% | 0.00% | C -> T |
mr1016 (Jap_All); LR P-value: 1.89E-09;
mr1017 (Jap_All); LR P-value: 2.71E-10; mr1018 (Jap_All); LR P-value: 5.73E-10; mr1055 (Jap_All); LR P-value: 7.02E-11; mr1390 (Jap_All); LR P-value: 1.71E-10; mr1490 (Jap_All); LR P-value: 8.73E-12; mr1055_2 (Jap_All); LR P-value: 1.72E-12; mr1132_2 (Jap_All); LR P-value: 1.02E-13; mr1390_2 (Jap_All); LR P-value: 4.78E-13; mr1490_2 (Jap_All); LR P-value: 9.11E-14 |
LOC_Os06g50250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.639; most accessible tissue: Zhenshan97 root, score: 75.661 |
| vg0630422651 (J) | chr06 | 30422651 | C | A | 94.00% | 0.00% | C -> A |
mr1498 (All); LR P-value: 6.84E-09;
mr1769 (All); LR P-value: 5.11E-11; mr1769 (Ind_All); LR P-value: 4.31E-10; mr1951 (All); LR P-value: 1.68E-09; mr1498_2 (All); LR P-value: 5.20E-14; mr1498_2 (Ind_All); LR P-value: 1.79E-09; mr1769_2 (All); LR P-value: 1.27E-10; mr1769_2 (Ind_All); LR P-value: 1.31E-10; mr1925_2 (All); LR P-value: 4.15E-08; mr1951_2 (All); LR P-value: 6.52E-10; mr1951_2 (Ind_All); LR P-value: 2.12E-08 |
LOC_Os06g50250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 54.466; most accessible tissue: Zhenshan97 root, score: 77.090 |
| vg0630422705 (J) | chr06 | 30422705 | A | C | 81.00% | 0.00% | C -> A |
LOC_Os06g50250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 58.331; most accessible tissue: Callus, score: 84.111 |
|
| vg0630422795 (J) | chr06 | 30422795 | C | A | 51.10% | 0.00% | C -> A |
mr1016 (Jap_All); LR P-value: 1.89E-09;
mr1017 (Jap_All); LR P-value: 2.71E-10; mr1018 (Jap_All); LR P-value: 5.73E-10; mr1055 (Jap_All); LR P-value: 7.02E-11; mr1390 (Jap_All); LR P-value: 1.71E-10; mr1490 (Jap_All); LR P-value: 8.73E-12; mr1055_2 (Jap_All); LR P-value: 1.72E-12; mr1132_2 (Jap_All); LR P-value: 1.02E-13; mr1390_2 (Jap_All); LR P-value: 4.78E-13; mr1490_2 (Jap_All); LR P-value: 9.11E-14 |
LOC_Os06g50250.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 59.408; most accessible tissue: Callus, score: 84.111 |
| vg0630422904 (J) | chr06 | 30422904 | CTTGGTC TTGCGA | C | 99.60% | 0.00% | CTTGGTCTTG CGA -> C | NA |
LOC_Os06g50250.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 55.223; most accessible tissue: Zhenshan97 root, score: 75.661 |
| vg0630422972 (J) | chr06 | 30422972 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os06g50240.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os06g50260.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g50230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g50250.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.719; most accessible tissue: Callus, score: 81.891 |
| vg0630423052 (J) | chr06 | 30423052 | T | C | 59.50% | 0.00% | C -> T |
mr1016 (Jap_All); LR P-value: 1.89E-09;
mr1017 (Jap_All); LR P-value: 2.71E-10; mr1018 (Jap_All); LR P-value: 5.73E-10; mr1055 (Jap_All); LR P-value: 7.02E-11; mr1162 (All); LR P-value: 1.85E-07; mr1390 (Jap_All); LR P-value: 1.71E-10; mr1490 (Jap_All); LR P-value: 8.73E-12; mr1803 (All); LR P-value: 2.73E-06; mr1055_2 (Jap_All); LR P-value: 1.72E-12; mr1132_2 (Jap_All); LR P-value: 1.02E-13; mr1390_2 (Jap_All); LR P-value: 4.78E-13; mr1490_2 (Jap_All); LR P-value: 9.11E-14; mr1749_2 (All); LR P-value: 2.18E-07; mr1821_2 (All); LR P-value: 1.18E-07 |
LOC_Os06g50260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g50230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g50240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g50250.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.579; most accessible tissue: Callus, score: 81.891 |
| vg0630423181 (J) | chr06 | 30423181 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os06g50260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g50230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g50240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g50250.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 42.911; most accessible tissue: Callus, score: 84.044 |
| vg0630423186 (J) | chr06 | 30423186 | T | A | 79.80% | 0.00% | A -> T |
mr1364 (All); LR P-value: 1.55E-07;
mr1364 (Jap_All); LR P-value: 4.67E-06; mr1443 (All); LR P-value: 3.95E-07; mr1443 (Jap_All); LR P-value: 3.40E-07; mr1518 (Jap_All); LR P-value: 3.33E-06; mr1533 (All); LR P-value: 2.67E-38; mr1659 (All); LR P-value: 3.06E-07; mr1980 (All); LR P-value: 1.96E-32; mr1261_2 (All); LR P-value: 1.66E-52; mr1533_2 (All); LR P-value: 4.75E-40; mr1980_2 (All); LR P-value: 1.11E-19 |
LOC_Os06g50260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g50230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g50240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g50250.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.755; most accessible tissue: Callus, score: 84.044 |
| STR0630422631 (J) | chr06 | 30422631 | CTTCTTT | CTTCTTC | 49.20% | 0.00% | CTTCTTC -> CTTCTTT | NA |
|