# Bismark Processing Report

### SRR5008109_WGBS_Seq_E14_d11_1_control_1_val_1.fq.gz and SRR5008109_WGBS_Seq_E14_d11_1_control_2_val_2.fq.gz

Data processed at 11:25 on 2018-08-16

## Alignment Stats

Sequence pairs analysed in total | 9399055
Paired-end alignments with a unique best hit | 7018098
Pairs without alignments under any condition | 1722286
Pairs that did not map uniquely | 658671
Genomic sequence context not extractable (edges of chromosomes) | 6

## Cytosine Methylation

Total C's analysed | 264469464
Methylated C's in CpG context | 8364359
Methylated C's in CHG context | 755431
Methylated C's in CHH context | 2166832
Methylated C's in Unknown context | 535
Unmethylated C's in CpG context | 3380818
Unmethylated C's in CHG context | 57592010
Unmethylated C's in CHH context | 192210014
Unmethylated C's in Unknown context | 56967
Percentage methylation (CpG context) | 71.2%
Percentage methylation (CHG context) | 1.3%
Percentage methylation (CHH context) | 1.1%
Methylated C's in Unknown context | N/A%

## Alignment to Individual Bisulfite Strands

OT | 3544531 | original top strand
CTOT | 0 | complementary to original top strand
CTOB | 0 | complementary to original bottom strand
OB | 3473561 | original bottom strand

## Deduplication

Alignments analysed | 7018092
Unique alignments | 6598101
Duplicates removed | 419991
Duplicated alignments were found at 338524 different positions

## Cytosine Methylation after Extraction

Total C's analysed | 241956905
Methylated C's in CpG context | 7173286
Methylated C's in CHG context | 681193
Methylated C's in CHH context | 1884937
Unmethylated C's in CpG context | 2915868
Unmethylated C's in CHG context | 52772247
Unmethylated C's in CHH context | 176529374
Percentage methylation (CpG context) | 71.1%
Percentage methylation (CHG context) | 1.3%
Percentage methylation (CHH context) | 1.1%

## M-Bias Plot