Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM02-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM02-Larvae_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 53188835
Paired-end alignments with a unique best hit 19330848
Pairs without alignments under any condition 24520436
Pairs that did not map uniquely 9337551
Genomic sequence context not extractable (edges of chromosomes) 7

Cytosine Methylation

Total C's analysed 615791768
Methylated C's in CpG context 19028347
Methylated C's in CHG context 2948221
Methylated C's in CHH context 13301236
Methylated C's in Unknown context 449219
Unmethylated C's in CpG context 72906143
Unmethylated C's in CHG context 127811018
Unmethylated C's in CHH context 379796803
Unmethylated C's in Unknown context 2683254
Percentage methylation (CpG context) 20.7%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 3.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4734689 original top strand
CTOT 4932868 complementary to original top strand
CTOB 4931784 complementary to original bottom strand
OB 4731500 original bottom strand

Deduplication

Alignments analysed 19330841
Unique alignments 14433376
Duplicates removed 4897465
Duplicated alignments were found at 3660302 different positions

Cytosine Methylation after Extraction

Total C's analysed 254099662
Methylated C's in CpG context 7737892
Methylated C's in CHG context 1276886
Methylated C's in CHH context 5710580
Unmethylated C's in CpG context 29947094
Unmethylated C's in CHG context 52390291
Unmethylated C's in CHH context 157036919
Percentage methylation (CpG context) 20.5%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 3.5%

M-Bias Plot