12 variations found. LOC_Os02g44080 (aquaporin protein; putative; expressed), ranging from 26,608,360 bp to 26,609,658 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0226608386 (J) | chr02 | 26608386 | T | C | 52.60% | 0.00% | C -> T |
mr1609 (All); LR P-value: 4.06E-11;
mr1713 (All); LR P-value: 1.81E-11; mr1133_2 (All); LR P-value: 2.35E-14; mr1148_2 (All); LR P-value: 1.43E-15; mr1227_2 (All); LR P-value: 1.61E-07; mr1272_2 (All); LR P-value: 1.05E-07; mr1349_2 (Ind_All); LR P-value: 6.29E-06; mr1479_2 (All); LR P-value: 1.43E-08; mr1726_2 (All); LR P-value: 1.58E-14; mr1835_2 (All); LR P-value: 1.18E-09; mr1836_2 (All); LR P-value: 9.10E-16; mr1871_2 (Ind_All); LR P-value: 2.93E-06; mr1895_2 (Ind_All); LR P-value: 1.82E-06; mr1904_2 (All); LR P-value: 3.64E-13 |
LOC_Os02g44080.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 43.419; most accessible tissue: Minghui63 root, score: 58.187 |
| vg0226608559 (J) | chr02 | 26608559 | AAACGGA ATTGGAA GTTGTTC GGTCAAG TATAGGA AATT | A | 50.40% | 0.00% | A -> AAACGGAATT GGAAGTTGTT CGGTCAAGTA TAGGAAATT | NA |
The average chromatin accessibility score: 68.656; most accessible tissue: Minghui63 panicle, score: 81.412
|
| vg0226608561 (J) | chr02 | 26608561 | A | ACGGAAT TGGAAGT TGTTCGG | 99.40% | 0.00% | A -> ACGGAAT,AC GGAATTGGAA GTTGTTCGG, ACGGAATTGG AAGTTGT,AC GGAATTGGAA GTTG,ACGGA ATTGGAAG,A CGGAATTGGA AGT | NA |
LOC_Os02g44080.1 Alt: ACGGAATTGGAAGTTG| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g44080.1 Alt: ACGGAATTGGAAG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g44080.1 Alt: ACGGAAT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g44080.1 Alt: ACGGAATTGGAAGTTGTTCGG| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g44080.1 Alt: ACGGAATTGGAAGTTGT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g44080.1 Alt: ACGGAATTGGAAGT| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.411; most accessible tissue: Minghui63 panicle, score: 80.641 |
| vg0226608626 (J) | chr02 | 26608626 | T | C | 99.00% | 0.00% | T -> C | NA |
LOC_Os02g44080.1 Alt: C| stop_retained_variant LOW(snpEff)
The average chromatin accessibility score: 71.600; most accessible tissue: Minghui63 panicle, score: 84.005 |
| vg0226608644 (J) | chr02 | 26608644 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g44080.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 72.979; most accessible tissue: Minghui63 panicle, score: 84.552 |
| vg0226609014 (J) | chr02 | 26609014 | G | A | 92.70% | 0.00% | G -> A |
mr1230 (All); LR P-value: 4.98E-06;
mr1278 (All); LR P-value: 4.84E-07; mr1424 (All); LR P-value: 7.34E-07; mr1438 (All); LR P-value: 7.83E-06; mr1884 (All); LR P-value: 2.91E-06; mr1871_2 (Ind_All); LR P-value: 5.59E-07; mr1892_2 (All); LR P-value: 4.29E-06; mr1895_2 (Ind_All); LR P-value: 4.58E-06; mr1919_2 (All); LMM P-value: 7.88E-06; LR P-value: 7.85E-06 |
LOC_Os02g44080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.876; most accessible tissue: Minghui63 panicle, score: 84.552 |
| vg0226609031 (J) | chr02 | 26609031 | A | G | 60.40% | 0.00% | G -> A | NA |
LOC_Os02g44080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.040; most accessible tissue: Minghui63 panicle, score: 84.552 |
| vg0226609424 (J) | chr02 | 26609424 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g44080.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.745; most accessible tissue: Zhenshan97 root, score: 86.891 |
| vg0226609449 (J) | chr02 | 26609449 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os02g44080.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 70.649; most accessible tissue: Zhenshan97 root, score: 86.362 |
| vg0226609469 (J) | chr02 | 26609469 | G | A | 60.40% | 0.00% | A -> G | NA |
LOC_Os02g44080.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.922; most accessible tissue: Zhenshan97 root, score: 86.891 |
| vg0226609582 (J) | chr02 | 26609582 | ATT | AT | 60.10% | 0.00% | AT -> ATT,A,ATTT | NA |
LOC_Os02g44080.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g44080.1 Alt: ATTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g44080.1 Alt: ATT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.730; most accessible tissue: Zhenshan97 root, score: 87.735 |
| vg0226609631 (J) | chr02 | 26609631 | G | A | 60.40% | 0.00% | A -> G | NA |
LOC_Os02g44080.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.005; most accessible tissue: Zhenshan97 root, score: 88.318 |