Input data and parameters 

Input

Analysis date: Wed Apr 27 20:00:21 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): 23,011,732 / 22,733,617
Number of aligned pairs (without duplicates): 20,735,972
Total number of alignments: 48,635,772
Number of secondary alignments: 2,890,423
Number of non-unique alignments: 4,601,142
Aligned to genes: 39,103,662
Ambiguous alignments: 352,759
No feature assigned: 4,577,916
Missing chromosome in annotation: 293
Not aligned: 1,808,371
Strand specificity estimation (fwd/rev): 0.5 / 0.5

Reads genomic origin

Exonic: 39,103,662 / 89.52%
Intronic: 3,240,596 / 7.42%
Intergenic: 1,337,320 / 3.06%
Intronic/intergenic overlapping exon: 971,103 / 2.22%

Transcript coverage profile

5' bias: 0.64
3' bias: 0.24
5'-3' bias: 1.61

Junction analysis

Reads at junctions: 24,666,458
AGGT 4.53%
ACCT 4.4%
AGGA 3.64%
AGGG 3.01%
TCCT 2.94%
AGCT 2.86%
CCCT 2.68%
AGAT 2.59%
AGAA 2.5%
ATCT 2.41%
AGGC 2.39%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis