Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0924/EPI-154_S5_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-154_S5_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 25217448
Paired-end alignments with a unique best hit 9258376
Pairs without alignments under any condition 13652807
Pairs that did not map uniquely 2306265
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 223981828
Methylated C's in CpG context 7732407
Methylated C's in CHG context 601411
Methylated C's in CHH context 2476347
Methylated C's in Unknown context 28441
Unmethylated C's in CpG context 21485179
Unmethylated C's in CHG context 46296623
Unmethylated C's in CHH context 145389861
Unmethylated C's in Unknown context 474204
Percentage methylation (CpG context) 26.5%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 1.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4559541 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4698835 original bottom strand

Deduplication

Alignments analysed 9258376
Unique alignments 6653225
Duplicates removed 2605151
Duplicated alignments were found at 1620665 different positions

Cytosine Methylation after Extraction

Total C's analysed 110479726
Methylated C's in CpG context 3874197
Methylated C's in CHG context 259536
Methylated C's in CHH context 1284370
Unmethylated C's in CpG context 10033498
Unmethylated C's in CHG context 22139548
Unmethylated C's in CHH context 72888577
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 1.2%
Percentage methylation (CHH context) 1.7%

M-Bias Plot