Input data and parameters 

Input

Analysis date: Wed Apr 27 19:35:55 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): 19,638,224 / 19,400,291
Number of aligned pairs (without duplicates): 17,448,415
Total number of alignments: 41,576,869
Number of secondary alignments: 2,538,354
Number of non-unique alignments: 4,014,499
Aligned to genes: 33,552,491
Ambiguous alignments: 319,971
No feature assigned: 3,689,669
Missing chromosome in annotation: 239
Not aligned: 1,681,519
Strand specificity estimation (fwd/rev): 0.5 / 0.5

Reads genomic origin

Exonic: 33,552,491 / 90.09%
Intronic: 2,504,852 / 6.73%
Intergenic: 1,184,817 / 3.18%
Intronic/intergenic overlapping exon: 846,106 / 2.27%

Transcript coverage profile

5' bias: 0.67
3' bias: 0.25
5'-3' bias: 1.58

Junction analysis

Reads at junctions: 21,301,122
AGGT 4.43%
ACCT 4.35%
AGGA 3.51%
AGGG 3.11%
TCCT 2.92%
CCCT 2.86%
AGCT 2.84%
AGAT 2.57%
AGAA 2.46%
ATCT 2.38%
AGGC 2.34%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis