BISMA results:

Reference sequence (original) : CTTCCCAAAGTGCTAGGATTATAGGCGTGAGCCTCCGCACCTGGCATGCCTGGCCATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATCCACGAAAGTAAAGTGCCTAGGGCCCATCAATGTCAGATGCAGCCACGTGGACAAAGAACACTCCCTGAGCA
Reference sequence (converted): TTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
Number CpG in Reference sequence: 4

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     
		

			

			
			
			                   2                   4                   6                   8                   0                   2                   4                   6     
		

			

			Number
			Sequence_id
			                   0                   0                   0                   0                   0                   0                   0                   0     
		

			

			
			Reference
			TTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
		

		
149KP-Hyal11R1selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA

		
250KP-Hyal11R2selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA

		
351KP-Hyal11R3selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA

	

	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
CpG position 26 36 94 137
Methylation [%] 100.0 100.0 100.0 100.0


CG site No.

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% (12 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (12 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
49KP-Hyal11R1selection 100.0
50KP-Hyal11R2selection 100.0
51KP-Hyal11R3selection 100.0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/19/13
Project name RWPE1 Endpoint Comparison
Tissue RWPE1
Gene or position Hyal1 #1