Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz

Data processed at 20:04 on 2019-08-12


Alignment Stats

Sequence pairs analysed in total 28905983
Paired-end alignments with a unique best hit 12331889
Pairs without alignments under any condition 14292877
Pairs that did not map uniquely 2281217
Genomic sequence context not extractable (edges of chromosomes) 3

Cytosine Methylation

Total C's analysed 389840146
Methylated C's in CpG context 12477704
Methylated C's in CHG context 1827358
Methylated C's in CHH context 3035063
Methylated C's in Unknown context 49011
Unmethylated C's in CpG context 45041606
Unmethylated C's in CHG context 80081549
Unmethylated C's in CHH context 247376866
Unmethylated C's in Unknown context 795814
Percentage methylation (CpG context) 21.7%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 1.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 6078960 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6252926 original bottom strand

Deduplication

Alignments analysed 12331886
Unique alignments 10413822
Duplicates removed 1918064
Duplicated alignments were found at 946129 different positions

Cytosine Methylation after Extraction

Total C's analysed 243953258
Methylated C's in CpG context 8558544
Methylated C's in CHG context 1135855
Methylated C's in CHH context 2017566
Unmethylated C's in CpG context 25838202
Unmethylated C's in CHG context 48531203
Unmethylated C's in CHH context 157871888
Percentage methylation (CpG context) 24.9%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 1.3%

M-Bias Plot