Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz and /gscratch/scrubbed/sr320/0821/Pg_val_2.fq.gz

Data processed at 07:08 on 2019-08-26


Alignment Stats

Sequence pairs analysed in total 1237279577
Paired-end alignments with a unique best hit 510447476
Pairs without alignments under any condition 612597329
Pairs that did not map uniquely 114234772
Genomic sequence context not extractable (edges of chromosomes) 86

Cytosine Methylation

Total C's analysed 15255999761
Methylated C's in CpG context 591642424
Methylated C's in CHG context 77274827
Methylated C's in CHH context 183983876
Methylated C's in Unknown context 3101698
Unmethylated C's in CpG context 1569847325
Unmethylated C's in CHG context 3194099749
Unmethylated C's in CHH context 9639151560
Unmethylated C's in Unknown context 32722537
Percentage methylation (CpG context) 27.4%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 252090696 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 258356694 original bottom strand

Deduplication

Alignments analysed 510447390
Unique alignments 273534856
Duplicates removed 236912534
Duplicated alignments were found at 82938427 different positions

Cytosine Methylation after Extraction

Total C's analysed 5902630221
Methylated C's in CpG context 235259793
Methylated C's in CHG context 28549310
Methylated C's in CHH context 81164170
Unmethylated C's in CpG context 561418412
Unmethylated C's in CHG context 1182055762
Unmethylated C's in CHH context 3814182774
Percentage methylation (CpG context) 29.5%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.1%

M-Bias Plot