BISMA results:

Reference sequence (original) : ACCAGGTTTCTGAGAACTGGCTCCTGATTCAGCAGCCAGCTAGCCCCACTCCCTTCCCAGAAGGTCTCTGAGCTTCATAAGGGACTTTCTGGAGCTTTCTGGGACTTTCTCTCACCCAGGCCCTCAACCTCCTCACCTGGAACTTTTCAGTAGCCCGCAGCCGCTCCTGCCAGCGGCCCTCCAACCTCTGTTCCAACGCTGCCCTGCGCTCCAGGAGGCCTCCGCGCTCAGCCTGGAGCTGCTGCAGCTC
Reference sequence (converted): ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
Number CpG in Reference sequence: 7

Parameters used:

Alignment mode: pairwise alignment of reference sequence and experimental sequences
Lower threshold conversion rate: 95%
Lower threshold sequence identity: 90%
Upper threshold of N-sites at cytosine positions: 20%
Upper threshold insertions/deletions: 20%

Final sequence alignment of the sequences included:

                                                                                                                                                                                                                                                              
                                                                                                   1                    1                   1                   1                   1                   2                   2                   2             
                   2                   4                   6                   8                   0                    2                   4                   6                   8                   0                   2                   4             
Number Sequence_id                    0                   0                   0                   0                   0                    0                   0                   0                   0                   0                   0                   0             
Reference ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
157KP-Nes1N7selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTGGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGTGTTTAGTTTGGAGTTGTTGTAGTTT
251KP-Nes1N1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAAGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
352KP-Nes1N2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
453KP-Nes1N3selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
554KP-Nes1N4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
655KP-Nes1N5selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
756KP-Nes1N6selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTGTTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
858KP-Nes1N8selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
960KP-Nes1N10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTTGTAGTTGTTTTTGTTAGTGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTTGTGTTTAGTTTGGAGTTGTTGTAGTTT
Legend: methylated CpG position unmethylated CpG position unconverted cytosine cytosine at unexpected position

Methylation pattern in subclones:

methylated  , unmethylated  , unknown 

Methylation status of CpG-sites cytosine in the sequence context


Methylation pattern



Average methylation for each CpG site:

CpG site 1 2 3 4 5 6 7
CpG position 156 162 174 197 207 223 225
Methylation [%] 0.0 0.0 0.0 0.0 0.0 11.1 0.0


CG site No.

0.0%0.0%0.0%0.0%0.0%11.1%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 98.4% (62 cases)
Methylated CpGs: 1.6% (1 case)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (63 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
57KP-Nes1N7selection 14.3
51KP-Nes1N1selection 0
52KP-Nes1N2selection 0
53KP-Nes1N3selection 0
54KP-Nes1N4selection 0
55KP-Nes1N5selection 0
56KP-Nes1N6selection 0
58KP-Nes1N8selection 0
60KP-Nes1N10selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/4/13
Project name RWPE1 Endpoint Comparison
Tissue Negative Control
Gene or position Nes #1