Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF06-CM02-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF06-CM02-Larvae_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 49423309
Paired-end alignments with a unique best hit 11862390
Pairs without alignments under any condition 31683507
Pairs that did not map uniquely 5877412
Genomic sequence context not extractable (edges of chromosomes) 8

Cytosine Methylation

Total C's analysed 331618841
Methylated C's in CpG context 11009460
Methylated C's in CHG context 3171557
Methylated C's in CHH context 17553182
Methylated C's in Unknown context 355014
Unmethylated C's in CpG context 33651900
Unmethylated C's in CHG context 62821831
Unmethylated C's in CHH context 203410911
Unmethylated C's in Unknown context 1649099
Percentage methylation (CpG context) 24.7%
Percentage methylation (CHG context) 4.8%
Percentage methylation (CHH context) 7.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3028128 original top strand
CTOT 2899793 complementary to original top strand
CTOB 2903454 complementary to original bottom strand
OB 3031007 original bottom strand

Deduplication

Alignments analysed 11862382
Unique alignments 8870215
Duplicates removed 2992167
Duplicated alignments were found at 2233561 different positions

Cytosine Methylation after Extraction

Total C's analysed 136935257
Methylated C's in CpG context 4543213
Methylated C's in CHG context 1383099
Methylated C's in CHH context 7586137
Unmethylated C's in CpG context 13817899
Unmethylated C's in CHG context 25699283
Unmethylated C's in CHH context 83905626
Percentage methylation (CpG context) 24.7%
Percentage methylation (CHG context) 5.1%
Percentage methylation (CHH context) 8.3%

M-Bias Plot