Input data and parameters 

Input

Analysis date: Mon Oct 30 09:43:07 GMT 2023
BAM file: SRX7354142.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): 44,340,367 / 44,316,511
Number of aligned pairs (without duplicates): 44,310,807
Total number of alignments: 97,107,115
Number of secondary alignments: 8,450,237
Number of non-unique alignments: 13,339,540
Aligned to genes: 73,334,836
Ambiguous alignments: 244,639
No feature assigned: 9,169,008
Missing chromosome in annotation: 1,019,092
Not aligned: 2,417,198

Reads genomic origin

Exonic: 73,334,836 / 88.89%
Intronic: 6,301,732 / 7.64%
Intergenic: 2,867,276 / 3.48%
Intronic/intergenic overlapping exon: 3,554,267 / 4.31%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.19
5'-3' bias: 2

Junction analysis

Reads at junctions: 22,498,601
ACCT 5.26%
AGGT 4.72%
ATCT 3.65%
AGGA 3.58%
TCCT 3.5%
GCCT 3.04%
AGCT 2.66%
CCCT 2.41%
AGGC 2.33%
AGAT 2.18%
TTCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis