Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz

Data processed at 14:11 on 2019-11-04


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 521
Pairs without alignments under any condition 99479
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 18303
Methylated C's in CpG context 55
Methylated C's in CHG context 232
Methylated C's in CHH context 88
Methylated C's in Unknown context 0
Unmethylated C's in CpG context 5528
Unmethylated C's in CHG context 5252
Unmethylated C's in CHH context 7148
Unmethylated C's in Unknown context 3
Percentage methylation (CpG context) 1.0%
Percentage methylation (CHG context) 4.2%
Percentage methylation (CHH context) 1.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 385 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 136 original bottom strand

Deduplication

Alignments analysed 521
Unique alignments 471
Duplicates removed 50
Duplicated alignments were found at 34 different positions

Cytosine Methylation after Extraction

Total C's analysed 10284
Methylated C's in CpG context 29
Methylated C's in CHG context 127
Methylated C's in CHH context 48
Unmethylated C's in CpG context 3058
Unmethylated C's in CHG context 2873
Unmethylated C's in CHH context 4149
Percentage methylation (CpG context) 0.9%
Percentage methylation (CHG context) 4.2%
Percentage methylation (CHH context) 1.1%

M-Bias Plot