Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz

Data processed at 18:21 on 2019-07-02

Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 46044
Pairs without alignments under any condition 41743
Pairs that did not map uniquely 12213
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1338618
Methylated C's in CpG context 56405
Methylated C's in CHG context 6815
Methylated C's in CHH context 48427
Methylated C's in Unknown context 650
Unmethylated C's in CpG context 126578
Unmethylated C's in CHG context 269457
Unmethylated C's in CHH context 830936
Unmethylated C's in Unknown context 2904
Percentage methylation (CpG context) 30.8%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 5.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 21802 original top strand
CTOT 1135 complementary to original top strand
CTOB 1187 complementary to original bottom strand
OB 21920 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 928067
Methylated C's in CpG context 39311
Methylated C's in CHG context 4688
Methylated C's in CHH context 31030
Unmethylated C's in CpG context 87650
Unmethylated C's in CHG context 186405
Unmethylated C's in CHH context 578983
Percentage methylation (CpG context) 31.0%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 5.1%

M-Bias Plot