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
127KP-Nes1B5bselectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTCATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
228KP-Nes1B7bselectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTTTATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
331KP-Nes1B1selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
434KP-Nes1B4selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTT-GCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
538KP-Nes1B8selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTT--AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGCTCGTAGCCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
632KP-Nes1B2selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTT--ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGTGTTTTAGGAGGTTTTCGCGTTTAGTTTGGAGTTGTTGTAGTTT
739KP-Nes1B9selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTTTAGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAACGTTGTTTTGCGTTTTAGGAGGTTTTCGTGTTTAGTTTGGAGTTGTTGTAGTTT
840KP-Nes1B10selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTTATTTTTTTTTT-AGAAGGTTTTTGAGTTTTATAAGGGATTTTTTGGAGTTTTTTGGGATTTTTTTTT-ATTTAGGTTTTTAATTTTTTTATTTGGAATTTTTTAGTAGTTCGTAGTCGTTTTTGTTAGCGGTTTTTTAATTTTTGTTTTAATGTTGTTTTGCGTTTTAAGAGGTTTTCGCGTTTAATTTGGAG------------
933KP-Nes1B3selectionATTAGGTTTTTGAGAATTGGTTTTTGATTTAGTAGTTAGTTAGTTTNATTTTTTTTTT-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 [%] 88.9 88.9 88.9 77.8 77.8 88.9 77.8


CG site No.

88.9%88.9%88.9%77.8%77.8%88.9%77.8%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 15.9% (10 cases)
Methylated CpGs: 84.1% (53 cases)
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 
27KP-Nes1B5bselection 100.0
28KP-Nes1B7bselection 100.0
31KP-Nes1B1selection 100.0
34KP-Nes1B4selection 100.0
38KP-Nes1B8selection 100.0
32KP-Nes1B2selection 85.7
39KP-Nes1B9selection 85.7
40KP-Nes1B10selection 85.7
33KP-Nes1B3selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 10/21/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position Nes #1