BISMA results:

Reference sequence (original) : TGGCCTTAGTGGCCAGAGCAGCTGCTGCATACACTTATCACAGGTTTCGGCTTTGTAAATTAATTCATCTGCAAATAGTGCACTGTCTCCAGGTACAAATTCGATGCTGGAGCACTGGTTTCTTAAGGATTTAAGTTTAAAGTCAAAGGCTTCCTGCCCTAGGTGTTACAAATAAGTAGTGTCGTTTTCTTTTTTTGCTCTGAGTTTGTTCATCCAATCGTATCCGAGTATGCAAATAAACTTTAGCCCGTGCAGATAAAAAAGGAACAAATAAAGCCAAGTGC
Reference sequence (converted): TGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTCGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
Number CpG in Reference sequence: 6

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                   2       
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8       
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0       
Reference TGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTCGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
151KP-Aldh1a11N1selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATCGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
253KP-Aldh1a11N3selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTT--TGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
356KP-Aldh1a11N6selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
460KP-Aldh1a11N10selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGCATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATCGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
559KP-Aldh1a11N9selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
657KP-Aldh1a11N7selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
758KP-Aldh1a11N8selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTT--TGTTTTGAGTTTGTTCATTTAGTTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
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
CpG position 48 102 183 219 225 249
Methylation [%] 71.4 0.0 28.6 28.6 0.0 14.3


CG site No.

71.4%0.0%28.6%28.6%0.0%14.3%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 76.2% (32 cases)
Methylated CpGs: 23.8% (10 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (42 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
51KP-Aldh1a11N1selection 50.0
53KP-Aldh1a11N3selection 33.3
56KP-Aldh1a11N6selection 33.3
60KP-Aldh1a11N10selection 33.3
59KP-Aldh1a11N9selection 16.7
57KP-Aldh1a11N7selection 0
58KP-Aldh1a11N8selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/20/13
Project name RWPE1 Endpoint Comparison
Tissue Negative Control
Gene or position Aldh1a1 #1