50 variations found. LOC_Os01g10590 (osFTL8 FT-Like8 homologous to Flowering Locus T gene%3B contains Pfam profile PF01161%3A Phosphatidylethanolamine-binding protein; expressed), ranging from 5,652,592 bp to 5,655,352 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 |
---|---|---|---|---|---|---|---|---|---|
STR0105653340 (J) | chr01 | 5653340 | AAAACAA AAC | AAAACAA AA | 70.50% | 0.00% | AAAACAAAAC -> AAAACAAAA | NA |
|
STR0105654036 (J) | chr01 | 5654036 | CT | CC | 68.00% | 0.00% | CT -> CC | NA |
|
vg0105652752 (J) | chr01 | 5652752 | G | C | 94.00% | 0.00% | G -> C |
LOC_Os01g10590.1 Alt: C/splice_donor_variant(CooVar)
The average chromatin accessibility score: 68.832; most accessible tissue: Zhenshan97 flower, score: 79.365 |
|
vg0105652761 (J) | chr01 | 5652761 | G | A | 96.10% | 0.00% | G -> A |
LOC_Os01g10590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.770; most accessible tissue: Zhenshan97 flower, score: 79.850 |
|
vg0105652782 (J) | chr01 | 5652782 | A | C | 62.60% | 0.00% | A -> C |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.910; most accessible tissue: Zhenshan97 flower, score: 80.311 |
|
vg0105653001 (J) | chr01 | 5653001 | A | T | 62.50% | 0.25% | A -> T |
LOC_Os01g10590.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 53.538; most accessible tissue: Callus, score: 83.521 |
|
vg0105653013 (J) | chr01 | 5653013 | T | A | 62.40% | 0.25% | T -> A |
LOC_Os01g10590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.251; most accessible tissue: Callus, score: 83.521 |
|
vg0105653222 (J) | chr01 | 5653222 | C | A | 77.10% | 0.00% | C -> A | NA |
LOC_Os01g10590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 47.011; most accessible tissue: Callus, score: 88.212 |
vg0105653226 (J) | chr01 | 5653226 | C | CTTT | 74.10% | 0.44% | C -> CTTT,CTTTT ,CT,CTT | NA |
LOC_Os01g10590.1 Alt: CTTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g10590.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g10590.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g10590.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.816; most accessible tissue: Callus, score: 88.212 |
vg0105653227 (J) | chr01 | 5653227 | AT | TT | 49.80% | 0.38% | AT -> ATT,ATTT,T T,ATTTT,A | NA |
LOC_Os01g10590.1 Alt: TT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g10590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g10590.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g10590.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g10590.1 Alt: ATTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 48.816; most accessible tissue: Callus, score: 88.212 |
vg0105653238 (J) | chr01 | 5653238 | G | T | 98.90% | 0.00% | G -> T | NA |
LOC_Os01g10590.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 46.556; most accessible tissue: Callus, score: 88.212 |
vg0105653344 (J) | chr01 | 5653344 | CA | C | 62.80% | 0.00% | CA -> C | NA |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.465; most accessible tissue: Callus, score: 65.847 |
vg0105653351 (J) | chr01 | 5653351 | GTCATGA GATCT | G | 94.00% | 0.00% | GTCATGAGAT CT -> G | NA |
LOC_Os01g10590.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.782; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
vg0105653471 (J) | chr01 | 5653471 | G | T | 81.70% | 0.23% | G -> T | NA |
LOC_Os01g10590.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.531; most accessible tissue: Callus, score: 82.889 |
vg0105653478 (J) | chr01 | 5653478 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g10590.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 51.493; most accessible tissue: Callus, score: 82.889 |
vg0105653492 (J) | chr01 | 5653492 | T | C | 62.50% | 0.25% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.142; most accessible tissue: Callus, score: 82.889 |
|
vg0105653647 (J) | chr01 | 5653647 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 44.536; most accessible tissue: Zhenshan97 flower, score: 57.454 |
vg0105653716 (J) | chr01 | 5653716 | C | A | 98.90% | 0.00% | C -> A | NA |
LOC_Os01g10590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 43.475; most accessible tissue: Callus, score: 76.338 |
vg0105653891 (J) | chr01 | 5653891 | A | G | 73.00% | 0.00% | A -> G | NA |
LOC_Os01g10590.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 38.388; most accessible tissue: Callus, score: 50.948 |
vg0105654023 (J) | chr01 | 5654023 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 39.970; most accessible tissue: Callus, score: 72.421 |
vg0105654037 (J) | chr01 | 5654037 | T | C | 62.50% | 0.00% | T -> C |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 38.372; most accessible tissue: Callus, score: 72.421 |
|
vg0105654226 (J) | chr01 | 5654226 | G | C | 62.80% | 0.00% | G -> C |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 28.017; most accessible tissue: Callus, score: 60.489 |
|
vg0105654314 (J) | chr01 | 5654314 | C | T | 55.70% | 0.00% | T -> C |
mr1498 (All); LMM P-value: 2.19E-11; LR P-value: 6.92E-17;
mr1498 (Ind_All); LMM P-value: 1.14E-09; LR P-value: 3.11E-18; mr1769 (Ind_All); LMM P-value: 3.65E-07; LR P-value: 5.09E-11; mr1795 (Ind_All); LR P-value: 6.58E-06; mr1925 (All); LMM P-value: 3.92E-07; mr1925 (Ind_All); LMM P-value: 2.41E-06; LR P-value: 8.72E-14; mr1951 (All); LR P-value: 2.59E-07; mr1951 (Ind_All); LMM P-value: 6.58E-07; LR P-value: 4.16E-12; mr1498_2 (All); LMM P-value: 3.19E-08; mr1498_2 (Ind_All); LMM P-value: 1.02E-06; LR P-value: 4.30E-16; mr1769_2 (Ind_All); LMM P-value: 3.56E-06; LR P-value: 4.48E-14; mr1925_2 (All); LMM P-value: 8.19E-09; mr1925_2 (Ind_All); LR P-value: 5.23E-13; mr1951_2 (All); LR P-value: 4.19E-07; mr1951_2 (Ind_All); LR P-value: 1.71E-11; mr1959_2 (Ind_All); LR P-value: 5.49E-06 |
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 28.106; most accessible tissue: Callus, score: 60.489 |
vg0105654355 (J) | chr01 | 5654355 | A | T | 98.70% | 0.30% | A -> T | NA |
LOC_Os01g10590.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 27.394; most accessible tissue: Minghui63 panicle, score: 46.754 |
vg0105654362 (J) | chr01 | 5654362 | C | A | 55.60% | 0.04% | A -> C |
mr1498 (All); LMM P-value: 6.96E-12; LR P-value: 2.17E-17;
mr1498 (Ind_All); LMM P-value: 3.52E-10; LR P-value: 2.91E-19; mr1769 (Ind_All); LMM P-value: 3.28E-07; LR P-value: 1.57E-11; mr1795 (Ind_All); LR P-value: 2.02E-06; mr1925 (All); LMM P-value: 3.28E-07; mr1925 (Ind_All); LMM P-value: 2.12E-06; LR P-value: 3.50E-14; mr1951 (All); LMM P-value: 8.17E-06; LR P-value: 1.23E-07; mr1951 (Ind_All); LMM P-value: 2.42E-07; LR P-value: 7.15E-13; mr1236_2 (Ind_All); LR P-value: 6.52E-06; mr1498_2 (All); LMM P-value: 8.80E-10; LR P-value: 2.18E-07; mr1498_2 (Ind_All); LMM P-value: 1.35E-08; LR P-value: 3.82E-18; mr1769_2 (Ind_All); LMM P-value: 4.91E-08; LR P-value: 1.40E-15; mr1795_2 (Ind_All); LR P-value: 2.52E-06; mr1925_2 (All); LMM P-value: 1.52E-09; LR P-value: 2.03E-06; mr1925_2 (Ind_All); LMM P-value: 2.19E-06; LR P-value: 3.58E-14; mr1951_2 (All); LR P-value: 8.41E-08; mr1951_2 (Ind_All); LR P-value: 4.33E-13; mr1959_2 (Ind_All); LR P-value: 1.22E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g10590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 27.565; most accessible tissue: Minghui63 panicle, score: 50.413 |
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