Input data and parameters 

Input

Analysis date: Wed Apr 27 20:16:33 CST 2022
BAM file: /dev/stdin
Counting algorithm: uniquely-mapped-reads
GTF file: /home/bayegy/Databases/transcriptome/references/mmu/GCF_000001635.27_GRCm39_genomic.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: non-strand-specific
Sorting performed: no

Summary 

Reads alignment

Number of mapped reads (left/right): 20,799,690 / 20,781,980
Number of aligned pairs (without duplicates): 19,191,138
Total number of alignments: 48,457,315
Number of secondary alignments: 6,875,645
Number of non-unique alignments: 9,849,799
Aligned to genes: 34,372,582
Ambiguous alignments: 260,455
No feature assigned: 3,974,407
Missing chromosome in annotation: 72
Not aligned: 1,051,878
Strand specificity estimation (fwd/rev): 0.5 / 0.5

Reads genomic origin

Exonic: 34,372,582 / 89.64%
Intronic: 1,757,524 / 4.58%
Intergenic: 2,216,883 / 5.78%
Intronic/intergenic overlapping exon: 719,239 / 1.88%

Transcript coverage profile

5' bias: 0.67
3' bias: 0.33
5'-3' bias: 1.45

Junction analysis

Reads at junctions: 23,741,627
ACCT 4.73%
AGGT 4.36%
TCCT 3.44%
AGCT 3.4%
ATCT 3.36%
AGGA 3.05%
GCCT 3.03%
AGGG 3.02%
AGGC 2.96%
CCCT 2.33%
AGAT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis