Input data and parameters 

Input

Analysis date: Sun Oct 29 01:52:12 GMT 2023
BAM file: SRX7354110.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): 42,220,712 / 42,025,629
Number of aligned pairs (without duplicates): 41,988,929
Total number of alignments: 91,067,854
Number of secondary alignments: 6,821,513
Number of non-unique alignments: 10,991,058
Aligned to genes: 59,990,235
Ambiguous alignments: 187,634
No feature assigned: 19,249,321
Missing chromosome in annotation: 649,606
Not aligned: 18,192,759

Reads genomic origin

Exonic: 59,990,235 / 75.71%
Intronic: 9,540,020 / 12.04%
Intergenic: 9,709,301 / 12.25%
Intronic/intergenic overlapping exon: 3,525,885 / 4.45%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.27
5'-3' bias: 1.69

Junction analysis

Reads at junctions: 19,307,242
ACCT 5.15%
AGGT 4.63%
TCCT 3.86%
ATCT 3.72%
AGGA 3.39%
GCCT 3.12%
CCCT 2.71%
AGCT 2.55%
TTCT 2.37%
AGGC 2.31%
AGAT 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis