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 ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
141KP-Nes1P1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
242KP-Nes1P2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTNAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGNGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
343KP-Nes1P3selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTCTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
444KP-Nes1P4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
545KP-Nes1P5selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGCTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
646KP-Nes1P6selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
747KP-Nes1P7selection------------------------------------------------NTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
848KP-Nes1P8selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTTAGAAGGTTCTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
949KP-Nes1P9selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
1050KP-Nes1P10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
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 [%] 100.0 100.0 100.0 100.0 100.0 100.0 100.0


CG site No.

100.0%100.0%100.0%100.0%100.0%100.0%100.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 0.0% (0 case)
Methylated CpGs: 100.0% (69 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 98.6% (69 cases)
CpGs not analyzed: 1.4% (1 case)


Average methylation for each clone:

Seq. identifier Average 
41KP-Nes1P1selection 100.0
42KP-Nes1P2selection 100.0
43KP-Nes1P3selection 100.0
44KP-Nes1P4selection 100.0
45KP-Nes1P5selection 100.0
46KP-Nes1P6selection 100.0
47KP-Nes1P7selection 100.0
48KP-Nes1P8selection 100.0
49KP-Nes1P9selection 100.0
50KP-Nes1P10selection 100.0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/4/13
Project name RwPE1 Endpoint Comparison
Tissue positive control
Gene or position Nes #1