Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF07-CM02-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF07-CM02-Zygote_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 60588756
Paired-end alignments with a unique best hit 7587682
Pairs without alignments under any condition 48271147
Pairs that did not map uniquely 4729927
Genomic sequence context not extractable (edges of chromosomes) 7

Cytosine Methylation

Total C's analysed 176275607
Methylated C's in CpG context 3938080
Methylated C's in CHG context 607095
Methylated C's in CHH context 9685016
Methylated C's in Unknown context 289267
Unmethylated C's in CpG context 17009743
Unmethylated C's in CHG context 30870019
Unmethylated C's in CHH context 114165654
Unmethylated C's in Unknown context 961142
Percentage methylation (CpG context) 18.8%
Percentage methylation (CHG context) 1.9%
Percentage methylation (CHH context) 7.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2112107 original top strand
CTOT 1728030 complementary to original top strand
CTOB 1685694 complementary to original bottom strand
OB 2061844 original bottom strand

Deduplication

Alignments analysed 7587675
Unique alignments 4996504
Duplicates removed 2591171
Duplicated alignments were found at 1484744 different positions

Cytosine Methylation after Extraction

Total C's analysed 64887224
Methylated C's in CpG context 1476446
Methylated C's in CHG context 210107
Methylated C's in CHH context 2571983
Unmethylated C's in CpG context 6422420
Unmethylated C's in CHG context 11624207
Unmethylated C's in CHH context 42582061
Percentage methylation (CpG context) 18.7%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 5.7%

M-Bias Plot