Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0924/EPI-160_S7_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-160_S7_L002_R2_001_val_2.20bp-trim.fq.gz

Data processed at 07:08 on 2019-09-26


Alignment Stats

Sequence pairs analysed in total 31886930
Paired-end alignments with a unique best hit 11802275
Pairs without alignments under any condition 16439992
Pairs that did not map uniquely 3644663
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 272689183
Methylated C's in CpG context 9254013
Methylated C's in CHG context 844540
Methylated C's in CHH context 2942224
Methylated C's in Unknown context 36933
Unmethylated C's in CpG context 27616194
Unmethylated C's in CHG context 56966486
Unmethylated C's in CHH context 175065726
Unmethylated C's in Unknown context 560307
Percentage methylation (CpG context) 25.1%
Percentage methylation (CHG context) 1.5%
Percentage methylation (CHH context) 1.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5797783 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6004491 original bottom strand

Deduplication

Alignments analysed 11802274
Unique alignments 8697606
Duplicates removed 3104668
Duplicated alignments were found at 1816178 different positions

Cytosine Methylation after Extraction

Total C's analysed 135145113
Methylated C's in CpG context 4717929
Methylated C's in CHG context 336994
Methylated C's in CHH context 1514462
Unmethylated C's in CpG context 12428913
Unmethylated C's in CHG context 27286022
Unmethylated C's in CHH context 88860793
Percentage methylation (CpG context) 27.5%
Percentage methylation (CHG context) 1.2%
Percentage methylation (CHH context) 1.7%

M-Bias Plot