Input data and parameters 

Input

Analysis date: Sun Oct 29 13:03:00 GMT 2023
BAM file: SRX7354193.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): 48,675,559 / 48,658,801
Number of aligned pairs (without duplicates): 48,655,482
Total number of alignments: 103,498,641
Number of secondary alignments: 6,164,281
Number of non-unique alignments: 9,590,359
Aligned to genes: 79,671,351
Ambiguous alignments: 274,876
No feature assigned: 13,183,519
Missing chromosome in annotation: 778,536
Not aligned: 1,720,638

Reads genomic origin

Exonic: 79,671,351 / 85.8%
Intronic: 8,715,007 / 9.39%
Intergenic: 4,468,512 / 4.81%
Intronic/intergenic overlapping exon: 3,295,311 / 3.55%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.28
5'-3' bias: 1.66

Junction analysis

Reads at junctions: 29,165,070
ACCT 4.95%
AGGT 4.58%
ATCT 3.69%
TCCT 3.53%
AGGA 3.37%
GCCT 3.36%
AGCT 2.95%
CCCT 2.66%
AGGC 2.36%
TTCT 2.15%
AGAT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis