Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz

Data processed at 08:32 on 2021-03-03


Alignment Stats

Sequence pairs analysed in total 74728031
Paired-end alignments with a unique best hit 46408800
Pairs without alignments under any condition 19238137
Pairs that did not map uniquely 9081094
Genomic sequence context not extractable (edges of chromosomes) 4942

Cytosine Methylation

Total C's analysed 1612267900
Methylated C's in CpG context 23601594
Methylated C's in CHG context 1411700
Methylated C's in CHH context 6082043
Methylated C's in Unknown context 58589
Unmethylated C's in CpG context 183507479
Unmethylated C's in CHG context 281398346
Unmethylated C's in CHH context 1116266738
Unmethylated C's in Unknown context 4025578
Percentage methylation (CpG context) 11.4%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 11572791 original top strand
CTOT 11651127 complementary to original top strand
CTOB 11633070 complementary to original bottom strand
OB 11546870 original bottom strand

Deduplication

Alignments analysed 46403858
Unique alignments 37965474
Duplicates removed 8438384
Duplicated alignments were found at 7046567 different positions

Cytosine Methylation after Extraction

Total C's analysed 906239667
Methylated C's in CpG context 12856588
Methylated C's in CHG context 779982
Methylated C's in CHH context 3380492
Unmethylated C's in CpG context 102427741
Unmethylated C's in CHG context 156416133
Unmethylated C's in CHH context 630378731
Percentage methylation (CpG context) 11.2%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot