4 variations found. LOC_Os07g07400 (zinc finger A20 and AN1 domain-containing stress-associated protein; putative; expressed), ranging from 3,698,669 bp to 3,699,128 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0703698831 (J) | chr07 | 3698831 | T | C | 95.60% | 0.00% | T -> C |
mr1073 (All); LR P-value: 6.06E-06;
mr1113 (All); LR P-value: 6.29E-16; mr1184 (All); LR P-value: 2.01E-06; mr1409 (All); LR P-value: 1.73E-11; mr1549 (All); LR P-value: 3.03E-37; mr1757 (All); LR P-value: 4.51E-39; mr1409_2 (All); LR P-value: 3.03E-12; mr1510_2 (All); LR P-value: 3.37E-08; mr1549_2 (All); LR P-value: 8.08E-35; mr1550_2 (All); LR P-value: 1.00E-47; mr1740_2 (All); LR P-value: 3.60E-06; mr1757_2 (All); LR P-value: 9.29E-27; mr1762_2 (All); LR P-value: 3.51E-06 |
LOC_Os07g07400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.887; most accessible tissue: Zhenshan97 flower, score: 98.069 |
| vg0703698854 (J) | chr07 | 3698854 | A | G | 96.20% | 0.00% | A -> G | NA |
LOC_Os07g07400.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.685; most accessible tissue: Zhenshan97 flower, score: 98.016 |
| vg0703698863 (J) | chr07 | 3698863 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os07g07400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 90.860; most accessible tissue: Zhenshan97 flower, score: 98.069 |
| vg0703698944 (J) | chr07 | 3698944 | T | C | 98.50% | 0.00% | T -> C | NA |
LOC_Os07g07400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.790; most accessible tissue: Zhenshan97 flower, score: 98.039 |