Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-CM01-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-CM01-Zygote_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 32105151
Paired-end alignments with a unique best hit 4636366
Pairs without alignments under any condition 24877118
Pairs that did not map uniquely 2591667
Genomic sequence context not extractable (edges of chromosomes) 10

Cytosine Methylation

Total C's analysed 104445771
Methylated C's in CpG context 2042686
Methylated C's in CHG context 232168
Methylated C's in CHH context 3647880
Methylated C's in Unknown context 104660
Unmethylated C's in CpG context 9965003
Unmethylated C's in CHG context 17465052
Unmethylated C's in CHH context 71092982
Unmethylated C's in Unknown context 689325
Percentage methylation (CpG context) 17.0%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 4.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 1252794 original top strand
CTOT 1075456 complementary to original top strand
CTOB 1067723 complementary to original bottom strand
OB 1240383 original bottom strand

Deduplication

Alignments analysed 4636356
Unique alignments 3408078
Duplicates removed 1228278
Duplicated alignments were found at 855500 different positions

Cytosine Methylation after Extraction

Total C's analysed 41089728
Methylated C's in CpG context 809455
Methylated C's in CHG context 90539
Methylated C's in CHH context 1196651
Unmethylated C's in CpG context 3963864
Unmethylated C's in CHG context 6906662
Unmethylated C's in CHH context 28122557
Percentage methylation (CpG context) 17.0%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 4.1%

M-Bias Plot