Input data and parameters 

Input

Analysis date: Tue Oct 31 09:26:58 GMT 2023
BAM file: SRX7354305.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): 48,357,489 / 48,321,369
Number of aligned pairs (without duplicates): 48,307,671
Total number of alignments: 105,170,663
Number of secondary alignments: 8,491,805
Number of non-unique alignments: 12,842,435
Aligned to genes: 82,044,639
Ambiguous alignments: 342,911
No feature assigned: 8,856,386
Missing chromosome in annotation: 1,084,292
Not aligned: 3,282,692

Reads genomic origin

Exonic: 82,044,639 / 90.26%
Intronic: 5,437,612 / 5.98%
Intergenic: 3,418,774 / 3.76%
Intronic/intergenic overlapping exon: 4,056,545 / 4.46%

Transcript coverage profile

5' bias: 0.11
3' bias: 0.14
5'-3' bias: 1.84

Junction analysis

Reads at junctions: 30,145,166
ACCT 5.34%
TCCT 5.06%
AGGT 4.47%
ATCT 4.08%
AGGA 3.02%
CCCT 2.91%
GCCT 2.35%
AGGC 2.22%
AGCT 2.03%
TTCT 1.9%
TCCC 1.89%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis