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 ATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
111KP-Nes1C1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
212KP-Nes1C2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
316KP-Nes1C6selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTCTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTCTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
418KP-Nes1C8selection-TTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
520KP-Nes1C10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
613KP-Nes1C3selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
719KP-Nes1C9selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
814KP-Nes1C4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTT-AGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
915KP-Nes1C5selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
1017KP-Nes1C7selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
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 50.0 70.0 100.0 100.0


CG site No.

100.0%100.0%100.0%50.0%70.0%100.0%100.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 11.4% (8 cases)
Methylated CpGs: 88.6% (62 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (70 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
11KP-Nes1C1selection 100.0
12KP-Nes1C2selection 100.0
16KP-Nes1C6selection 100.0
18KP-Nes1C8selection 100.0
20KP-Nes1C10selection 100.0
13KP-Nes1C3selection 85.7
19KP-Nes1C9selection 85.7
14KP-Nes1C4selection 71.4
15KP-Nes1C5selection 71.4
17KP-Nes1C7selection 71.4



Experiment Documentation

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