Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz

Data processed at 02:53 on 2020-01-03


Alignment Stats

Sequence pairs analysed in total 21160872
Paired-end alignments with a unique best hit 9316819
Pairs without alignments under any condition 10036514
Pairs that did not map uniquely 1807539
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 288290011
Methylated C's in CpG context 10342749
Methylated C's in CHG context 1387455
Methylated C's in CHH context 2413979
Methylated C's in Unknown context 44158
Unmethylated C's in CpG context 29588909
Unmethylated C's in CHG context 58728884
Unmethylated C's in CHH context 185828035
Unmethylated C's in Unknown context 610790
Percentage methylation (CpG context) 25.9%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 1.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4624000 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4692818 original bottom strand

Deduplication

Alignments analysed 9316818
Unique alignments 7896079
Duplicates removed 1420739
Duplicated alignments were found at 811691 different positions

Cytosine Methylation after Extraction

Total C's analysed 180013500
Methylated C's in CpG context 6934397
Methylated C's in CHG context 872844
Methylated C's in CHH context 1579087
Unmethylated C's in CpG context 17647358
Unmethylated C's in CHG context 35893215
Unmethylated C's in CHH context 117086599
Percentage methylation (CpG context) 28.2%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.3%

M-Bias Plot