Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0924/EPI-153_S4_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-153_S4_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 25991438
Paired-end alignments with a unique best hit 10175887
Pairs without alignments under any condition 13072103
Pairs that did not map uniquely 2743448
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 243457431
Methylated C's in CpG context 8243304
Methylated C's in CHG context 719127
Methylated C's in CHH context 2417271
Methylated C's in Unknown context 27300
Unmethylated C's in CpG context 24883753
Unmethylated C's in CHG context 51417874
Unmethylated C's in CHH context 155776102
Unmethylated C's in Unknown context 496309
Percentage methylation (CpG context) 24.9%
Percentage methylation (CHG context) 1.4%
Percentage methylation (CHH context) 1.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5024225 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5151662 original bottom strand

Deduplication

Alignments analysed 10175887
Unique alignments 6548869
Duplicates removed 3627018
Duplicated alignments were found at 2034097 different positions

Cytosine Methylation after Extraction

Total C's analysed 104820913
Methylated C's in CpG context 3698740
Methylated C's in CHG context 269714
Methylated C's in CHH context 1131240
Unmethylated C's in CpG context 9618215
Unmethylated C's in CHG context 21506774
Unmethylated C's in CHH context 68596230
Percentage methylation (CpG context) 27.8%
Percentage methylation (CHG context) 1.2%
Percentage methylation (CHH context) 1.6%

M-Bias Plot