Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM04-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM04-Larvae_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 57667284
Paired-end alignments with a unique best hit 25131000
Pairs without alignments under any condition 19755662
Pairs that did not map uniquely 12780622
Genomic sequence context not extractable (edges of chromosomes) 13

Cytosine Methylation

Total C's analysed 849535844
Methylated C's in CpG context 22926977
Methylated C's in CHG context 2029014
Methylated C's in CHH context 10201931
Methylated C's in Unknown context 286774
Unmethylated C's in CpG context 97913175
Unmethylated C's in CHG context 171554242
Unmethylated C's in CHH context 544910505
Unmethylated C's in Unknown context 3165460
Percentage methylation (CpG context) 19.0%
Percentage methylation (CHG context) 1.2%
Percentage methylation (CHH context) 1.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 6016951 original top strand
CTOT 6529185 complementary to original top strand
CTOB 6558200 complementary to original bottom strand
OB 6026651 original bottom strand

Deduplication

Alignments analysed 25130987
Unique alignments 13915567
Duplicates removed 11215420
Duplicated alignments were found at 5950185 different positions

Cytosine Methylation after Extraction

Total C's analysed 286520198
Methylated C's in CpG context 7059413
Methylated C's in CHG context 662641
Methylated C's in CHH context 3451337
Unmethylated C's in CpG context 32490932
Unmethylated C's in CHG context 56079819
Unmethylated C's in CHH context 186776056
Percentage methylation (CpG context) 17.8%
Percentage methylation (CHG context) 1.2%
Percentage methylation (CHH context) 1.8%

M-Bias Plot