Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3644_9_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_9_R2.fastp-trim.20201206.fq.gz

Data processed at 14:16 on 2021-02-17


Alignment Stats

Sequence pairs analysed in total 47320068
Paired-end alignments with a unique best hit 18360604
Pairs without alignments under any condition 24005782
Pairs that did not map uniquely 4953682
Genomic sequence context not extractable (edges of chromosomes) 767

Cytosine Methylation

Total C's analysed 640786458
Methylated C's in CpG context 10549037
Methylated C's in CHG context 492224
Methylated C's in CHH context 1931100
Methylated C's in Unknown context 4507
Unmethylated C's in CpG context 73068267
Unmethylated C's in CHG context 114281671
Unmethylated C's in CHH context 440464159
Unmethylated C's in Unknown context 431083
Percentage methylation (CpG context) 12.6%
Percentage methylation (CHG context) 0.4%
Percentage methylation (CHH context) 0.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4626246 original top strand
CTOT 4555151 complementary to original top strand
CTOB 4555509 complementary to original bottom strand
OB 4622931 original bottom strand

Deduplication

Alignments analysed 18359837
Unique alignments 16135565
Duplicates removed 2224272
Duplicated alignments were found at 1958926 different positions

Cytosine Methylation after Extraction

Total C's analysed 360970772
Methylated C's in CpG context 5802078
Methylated C's in CHG context 274442
Methylated C's in CHH context 1088151
Unmethylated C's in CpG context 40875939
Unmethylated C's in CHG context 63778463
Unmethylated C's in CHH context 249151699
Percentage methylation (CpG context) 12.4%
Percentage methylation (CHG context) 0.4%
Percentage methylation (CHH context) 0.4%

M-Bias Plot