Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF02-CM02-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF02-CM02-Zygote_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 67063678
Paired-end alignments with a unique best hit 10105983
Pairs without alignments under any condition 50657462
Pairs that did not map uniquely 6300233
Genomic sequence context not extractable (edges of chromosomes) 6

Cytosine Methylation

Total C's analysed 188887969
Methylated C's in CpG context 4107683
Methylated C's in CHG context 1286993
Methylated C's in CHH context 13086957
Methylated C's in Unknown context 266487
Unmethylated C's in CpG context 16031720
Unmethylated C's in CHG context 29129543
Unmethylated C's in CHH context 125245073
Unmethylated C's in Unknown context 1213471
Percentage methylation (CpG context) 20.4%
Percentage methylation (CHG context) 4.2%
Percentage methylation (CHH context) 9.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3000851 original top strand
CTOT 2072592 complementary to original top strand
CTOB 2052690 complementary to original bottom strand
OB 2979844 original bottom strand

Deduplication

Alignments analysed 10105977
Unique alignments 6954232
Duplicates removed 3151745
Duplicated alignments were found at 2050943 different positions

Cytosine Methylation after Extraction

Total C's analysed 68800747
Methylated C's in CpG context 1494479
Methylated C's in CHG context 469414
Methylated C's in CHH context 4346748
Unmethylated C's in CpG context 5899332
Unmethylated C's in CHG context 10629429
Unmethylated C's in CHH context 45961345
Percentage methylation (CpG context) 20.2%
Percentage methylation (CHG context) 4.2%
Percentage methylation (CHH context) 8.6%

M-Bias Plot