Input data and parameters 

Input

Analysis date: Tue Oct 31 10:34:02 GMT 2023
BAM file: SRX7354333.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): 93,225,169 / 93,121,755
Number of aligned pairs (without duplicates): 93,111,872
Total number of alignments: 199,686,523
Number of secondary alignments: 13,339,599
Number of non-unique alignments: 20,180,971
Aligned to genes: 147,666,855
Ambiguous alignments: 572,738
No feature assigned: 29,367,149
Missing chromosome in annotation: 1,898,810
Not aligned: 15,040,988

Reads genomic origin

Exonic: 147,666,855 / 83.41%
Intronic: 17,610,531 / 9.95%
Intergenic: 11,756,618 / 6.64%
Intronic/intergenic overlapping exon: 7,082,759 / 4%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.3
5'-3' bias: 1.77

Junction analysis

Reads at junctions: 69,055,608
ACCT 5.01%
AGGT 4.93%
ATCT 3.54%
TCCT 3.53%
AGGA 3.31%
GCCT 2.8%
CCCT 2.63%
AGCT 2.62%
AGGC 2.51%
TTCT 2.32%
AGGG 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis