Input data and parameters 

Input

Analysis date: Tue Oct 31 09:52:45 GMT 2023
BAM file: SRX7354312.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.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: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 55,368,107 / 55,155,603
Number of aligned pairs (without duplicates): 55,120,104
Total number of alignments: 124,092,572
Number of secondary alignments: 13,568,862
Number of non-unique alignments: 17,328,367
Aligned to genes: 77,991,680
Ambiguous alignments: 315,486
No feature assigned: 25,175,853
Missing chromosome in annotation: 3,281,186
Not aligned: 14,242,764

Reads genomic origin

Exonic: 77,991,680 / 75.6%
Intronic: 13,694,504 / 13.27%
Intergenic: 11,481,349 / 11.13%
Intronic/intergenic overlapping exon: 4,859,254 / 4.71%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.2
5'-3' bias: 1.67

Junction analysis

Reads at junctions: 30,403,066
ACCT 5.07%
AGGT 4.54%
TCCT 3.92%
ATCT 3.63%
AGGA 3.16%
GCCT 3.07%
CCCT 2.65%
AGCT 2.35%
TTCT 2.27%
AGGC 2.26%
AGGG 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