Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM04-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM04-Zygote_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 70141415
Paired-end alignments with a unique best hit 9554896
Pairs without alignments under any condition 54144932
Pairs that did not map uniquely 6441587
Genomic sequence context not extractable (edges of chromosomes) 24

Cytosine Methylation

Total C's analysed 179687816
Methylated C's in CpG context 3894966
Methylated C's in CHG context 1072401
Methylated C's in CHH context 8124397
Methylated C's in Unknown context 288360
Unmethylated C's in CpG context 18819198
Unmethylated C's in CHG context 30837097
Unmethylated C's in CHH context 116939757
Unmethylated C's in Unknown context 1597788
Percentage methylation (CpG context) 17.1%
Percentage methylation (CHG context) 3.4%
Percentage methylation (CHH context) 6.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2369042 original top strand
CTOT 2422982 complementary to original top strand
CTOB 2410386 complementary to original bottom strand
OB 2352462 original bottom strand

Deduplication

Alignments analysed 9554872
Unique alignments 6882915
Duplicates removed 2671957
Duplicated alignments were found at 1902684 different positions

Cytosine Methylation after Extraction

Total C's analysed 67957021
Methylated C's in CpG context 1546006
Methylated C's in CHG context 497366
Methylated C's in CHH context 3097887
Unmethylated C's in CpG context 7085137
Unmethylated C's in CHG context 11636302
Unmethylated C's in CHH context 44094323
Percentage methylation (CpG context) 17.9%
Percentage methylation (CHG context) 4.1%
Percentage methylation (CHH context) 6.6%

M-Bias Plot