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 TGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTCGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
135KP-Aldh1a11B5selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAAATAAATAAAGTTAAGTGT
238KP-Aldh1a11B8selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAGATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
331KP-Aldh1a11B1selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
432KP-Aldh1a11B2selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
533KP-Aldh1a11B3selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTGTTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
634KP-Aldh1a11B4selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTGTTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
736KP-Aldh1a11B6selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTACTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
839KP-Aldh1a11B9selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
940KP-Aldh1a11B10selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTCTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAA-TAAATAAAGTTAAGTGT
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 [%] 22.2 0.0 0.0 0.0 0.0 0.0


CG site No.

22.2%0.0%0.0%0.0%0.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 96.3% (52 cases)
Methylated CpGs: 3.7% (2 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (54 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
35KP-Aldh1a11B5selection 16.7
38KP-Aldh1a11B8selection 16.7
31KP-Aldh1a11B1selection 0
32KP-Aldh1a11B2selection 0
33KP-Aldh1a11B3selection 0
34KP-Aldh1a11B4selection 0
36KP-Aldh1a11B6selection 0
39KP-Aldh1a11B9selection 0
40KP-Aldh1a11B10selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/20/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position Aldh1a1 #1