Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz

Data processed at 11:37 on 2019-08-07


Alignment Stats

Sequence pairs analysed in total 15453987
Paired-end alignments with a unique best hit 6380873
Pairs without alignments under any condition 7739907
Pairs that did not map uniquely 1333207
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 195385696
Methylated C's in CpG context 7804592
Methylated C's in CHG context 1021997
Methylated C's in CHH context 3443697
Methylated C's in Unknown context 54626
Unmethylated C's in CpG context 19140558
Unmethylated C's in CHG context 40545239
Unmethylated C's in CHH context 123429613
Unmethylated C's in Unknown context 431888
Percentage methylation (CpG context) 29.0%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3152381 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 3228492 original bottom strand

Deduplication

Alignments analysed 6380873
Unique alignments 4644265
Duplicates removed 1736608
Duplicated alignments were found at 1097543 different positions

Cytosine Methylation after Extraction

Total C's analysed 99137282
Methylated C's in CpG context 4217985
Methylated C's in CHG context 535634
Methylated C's in CHH context 1932988
Unmethylated C's in CpG context 9196803
Unmethylated C's in CHG context 20037165
Unmethylated C's in CHH context 63216707
Percentage methylation (CpG context) 31.4%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 3.0%

M-Bias Plot