Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz

Data processed at 17:55 on 2018-10-25


Alignment Stats

Sequence pairs analysed in total 10000
Paired-end alignments with a unique best hit 6152
Pairs without alignments under any condition 1905
Pairs that did not map uniquely 1943
Genomic sequence context not extractable (edges of chromosomes) 20

Cytosine Methylation

Total C's analysed 192465
Methylated C's in CpG context 6307
Methylated C's in CHG context 1051
Methylated C's in CHH context 9421
Methylated C's in Unknown context 343
Unmethylated C's in CpG context 22233
Unmethylated C's in CHG context 39408
Unmethylated C's in CHH context 114045
Unmethylated C's in Unknown context 1060
Percentage methylation (CpG context) 22.1%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 7.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2780 original top strand
CTOT 265 complementary to original top strand
CTOB 258 complementary to original bottom strand
OB 2829 original bottom strand

Deduplication

Alignments analysed 6132
Unique alignments 6085
Duplicates removed 47
Duplicated alignments were found at 32 different positions

Cytosine Methylation after Extraction

Total C's analysed 137497
Methylated C's in CpG context 4581
Methylated C's in CHG context 810
Methylated C's in CHH context 7064
Unmethylated C's in CpG context 15597
Unmethylated C's in CHG context 27779
Unmethylated C's in CHH context 81666
Percentage methylation (CpG context) 22.7%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 8.0%

M-Bias Plot