Input data and parameters 

Input

Analysis date: Tue Oct 31 15:38:32 GMT 2023
BAM file: SRX7354365.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): 33,042,844 / 32,998,712
Number of aligned pairs (without duplicates): 32,994,763
Total number of alignments: 71,436,516
Number of secondary alignments: 5,394,960
Number of non-unique alignments: 9,233,275
Aligned to genes: 55,428,180
Ambiguous alignments: 188,446
No feature assigned: 6,265,686
Missing chromosome in annotation: 320,929
Not aligned: 6,163,986

Reads genomic origin

Exonic: 55,428,180 / 89.84%
Intronic: 3,147,593 / 5.1%
Intergenic: 3,118,093 / 5.05%
Intronic/intergenic overlapping exon: 1,917,589 / 3.11%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.21
5'-3' bias: 1.95

Junction analysis

Reads at junctions: 16,378,852
ACCT 5.51%
AGGT 4.52%
ATCT 4.46%
TCCT 3.66%
GCCT 3.48%
AGGA 3.27%
CCCT 2.8%
AGCT 2.46%
TTCT 2.37%
AGGC 2.28%
AGAT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis