Input data and parameters 

Input

Analysis date: Mon Oct 30 22:53:20 GMT 2023
BAM file: SRX7354267.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): 40,060,454 / 40,027,193
Number of aligned pairs (without duplicates): 40,022,528
Total number of alignments: 84,078,041
Number of secondary alignments: 3,990,394
Number of non-unique alignments: 6,962,113
Aligned to genes: 68,709,732
Ambiguous alignments: 189,588
No feature assigned: 8,022,791
Missing chromosome in annotation: 193,817
Not aligned: 5,885,935

Reads genomic origin

Exonic: 68,709,732 / 89.54%
Intronic: 3,954,970 / 5.15%
Intergenic: 4,067,821 / 5.3%
Intronic/intergenic overlapping exon: 2,899,092 / 3.78%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.14
5'-3' bias: 2.32

Junction analysis

Reads at junctions: 20,594,690
ACCT 5.57%
AGGT 4.8%
AGGA 3.68%
ATCT 3.62%
TCCT 3.45%
GCCT 2.91%
AGCT 2.69%
AGGC 2.4%
AGAT 2.34%
CCCT 2.23%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis