Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM05-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM05-Larvae_R2_001_val_2.fq.gz

Data processed at 00:16 on 2021-05-09


Alignment Stats

Sequence pairs analysed in total 48978052
Paired-end alignments with a unique best hit 17211018
Pairs without alignments under any condition 23481673
Pairs that did not map uniquely 8285361
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 576011240
Methylated C's in CpG context 17042772
Methylated C's in CHG context 3377754
Methylated C's in CHH context 14831225
Methylated C's in Unknown context 430560
Unmethylated C's in CpG context 69075608
Unmethylated C's in CHG context 118450863
Unmethylated C's in CHH context 353233018
Unmethylated C's in Unknown context 2500352
Percentage methylation (CpG context) 19.8%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 4.0%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4221351 original top strand
CTOT 4375606 complementary to original top strand
CTOB 4385737 complementary to original bottom strand
OB 4228322 original bottom strand

Deduplication

Alignments analysed 17211016
Unique alignments 13288199
Duplicates removed 3922817
Duplicated alignments were found at 3037186 different positions

Cytosine Methylation after Extraction

Total C's analysed 249748547
Methylated C's in CpG context 7298824
Methylated C's in CHG context 1548651
Methylated C's in CHH context 6743014
Unmethylated C's in CpG context 29813254
Unmethylated C's in CHG context 50953449
Unmethylated C's in CHH context 153391355
Percentage methylation (CpG context) 19.7%
Percentage methylation (CHG context) 2.9%
Percentage methylation (CHH context) 4.2%

M-Bias Plot