41 variations found. LOC_Os06g35940 (osFTL12 FT-Like12 homologous to Flowering Locus T gene%3B contains Pfam profile PF01161%3A Phosphatidylethanolamine-binding protein; expressed), ranging from 20,971,625 bp to 20,974,233 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 |
---|---|---|---|---|---|---|---|---|---|
STR0620971948 (J) | chr06 | 20971948 | GATCGAT CGAT | GATCGAT CGATCGA | 99.00% | 0.00% | GATCGATCGA T -> GATCGATCGA TCGA | NA |
|
vg0620971631 (J) | chr06 | 20971631 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os06g35940.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.326; most accessible tissue: Callus, score: 80.687 |
vg0620971657 (J) | chr06 | 20971657 | T | TACAAC | 97.70% | 0.44% | T -> TACAAC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g35940.1 Alt: TACAAC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.928; most accessible tissue: Callus, score: 80.687 |
vg0620971659 (J) | chr06 | 20971659 | TAACATA | T | 66.90% | 0.00% | T -> TAACATA,TA ,TAACATATA | NA |
LOC_Os06g35940.1 Alt: TAACATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g35940.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: TAACATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.928; most accessible tissue: Callus, score: 80.687 |
vg0620971681 (J) | chr06 | 20971681 | C | CTTAA | 98.60% | 0.00% | C -> CTTAA | NA |
The average chromatin accessibility score: 63.626; most accessible tissue: Callus, score: 94.336
|
vg0620971789 (J) | chr06 | 20971789 | TTA | T | 97.50% | 0.00% | TTA -> T | NA |
LOC_Os06g35940.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.552; most accessible tissue: Callus, score: 94.336 |
vg0620971808 (J) | chr06 | 20971808 | T | A | 68.20% | 0.00% | A -> T | NA |
LOC_Os06g35940.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.416; most accessible tissue: Callus, score: 94.336 |
vg0620971837 (J) | chr06 | 20971837 | C | CATATAT ATATATA TATATAT ATATATA TATATAT ATATATA TATAT | 63.80% | 6.90% | CATATATATA TATATATATA TATATATATA TATATATATA TATATAT -> C,CATATATA TATATATATA TAT,CAT,CA TATATATATA TATATAT,CA TATATAT | NA |
LOC_Os06g35940.1 Alt: CATATATATATATATATAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g35940.1 Alt: CATATATAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: CAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: CATATATATATATATATATAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.044; most accessible tissue: Callus, score: 86.085 |
vg0620971842 (J) | chr06 | 20971842 | A | ATGCATG AG | 0.60% | 96.00% | A -> ATGCATGAG | NA |
LOC_Os06g35940.1 Alt: ATGCATGAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.806; most accessible tissue: Callus, score: 86.085 |
vg0620971843 (J) | chr06 | 20971843 | T | TGCATG | 63.40% | 33.58% | T -> TGCATG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g35940.1 Alt: TGCATG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.864; most accessible tissue: Callus, score: 86.085 |
vg0620971844 (J) | chr06 | 20971844 | A | G | 63.50% | 33.64% | A -> G | NA |
LOC_Os06g35940.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.864; most accessible tissue: Callus, score: 86.085 |
vg0620971845 (J) | chr06 | 20971845 | T | C | 63.50% | 33.64% | T -> C | NA |
LOC_Os06g35940.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.914; most accessible tissue: Callus, score: 86.085 |
vg0620971951 (J) | chr06 | 20971951 | C | CGAA | 98.60% | 0.00% | C -> CGAA | NA |
The average chromatin accessibility score: 80.612; most accessible tissue: Callus, score: 91.677
|
vg0620972083 (J) | chr06 | 20972083 | A | G | 98.60% | 0.00% | A -> G | NA |
LOC_Os06g35940.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.155; most accessible tissue: Minghui63 root, score: 85.968 |
vg0620972140 (J) | chr06 | 20972140 | G | T | 98.60% | 0.00% | G -> T | NA |
LOC_Os06g35940.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.670; most accessible tissue: Minghui63 root, score: 82.511 |
vg0620972361 (J) | chr06 | 20972361 | T | G | 66.50% | 0.00% | G -> T | NA |
LOC_Os06g35940.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 58.012; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
vg0620972365 (J) | chr06 | 20972365 | C | T | 98.60% | 0.00% | C -> T | NA |
LOC_Os06g35940.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 55.277; most accessible tissue: Zhenshan97 flower, score: 66.020 |
vg0620972599 (J) | chr06 | 20972599 | A | G | 51.20% | 0.00% | G -> A | NA |
LOC_Os06g35940.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 30.423; most accessible tissue: Minghui63 flag leaf, score: 45.977 |
vg0620972717 (J) | chr06 | 20972717 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g35940.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 26.428; most accessible tissue: Callus, score: 63.970 |
vg0620972814 (J) | chr06 | 20972814 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os06g35940.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 28.849; most accessible tissue: Callus, score: 63.970 |
vg0620972848 (J) | chr06 | 20972848 | G | A | 55.50% | 0.00% | G -> A |
LOC_Os06g35940.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 25.617; most accessible tissue: Callus, score: 45.536 |
|
vg0620972897 (J) | chr06 | 20972897 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os06g35940.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 26.502; most accessible tissue: Zhenshan97 young leaf, score: 46.636 |
vg0620973061 (J) | chr06 | 20973061 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os06g35940.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 29.269; most accessible tissue: Callus, score: 69.426 |
vg0620973157 (J) | chr06 | 20973157 | TTTTTTG | T | 32.80% | 0.00% | T -> TTTTTTG,TT G,TTTTTTTG ,TTTTTG,TG ,TTTG | NA |
LOC_Os06g35940.1 Alt: TG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g35940.1 Alt: TTTTTTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: TTTTTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: TTTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: TTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g35940.1 Alt: TTTTTTTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.133; most accessible tissue: Minghui63 root, score: 49.234 |
vg0620973158 (J) | chr06 | 20973158 | C | T | 36.90% | 32.12% | C -> T | NA |
LOC_Os06g35940.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 34.435; most accessible tissue: Minghui63 root, score: 49.234 |
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