Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz

Data processed at 05:18 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 11003725
Paired-end alignments with a unique best hit 4103253
Pairs without alignments under any condition 6008199
Pairs that did not map uniquely 892273
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 125649607
Methylated C's in CpG context 4647874
Methylated C's in CHG context 682027
Methylated C's in CHH context 3288445
Methylated C's in Unknown context 50440
Unmethylated C's in CpG context 13300931
Unmethylated C's in CHG context 26446504
Unmethylated C's in CHH context 77283826
Unmethylated C's in Unknown context 276168
Percentage methylation (CpG context) 25.9%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 4.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2013443 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 2089810 original bottom strand

Deduplication

Alignments analysed 4103253
Unique alignments 2766273
Duplicates removed 1336980
Duplicated alignments were found at 804018 different positions

Cytosine Methylation after Extraction

Total C's analysed 57532394
Methylated C's in CpG context 2287343
Methylated C's in CHG context 323890
Methylated C's in CHH context 1768982
Unmethylated C's in CpG context 5639671
Unmethylated C's in CHG context 11658279
Unmethylated C's in CHH context 35854229
Percentage methylation (CpG context) 28.9%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 4.7%

M-Bias Plot