Input data and parameters 

Input

Analysis date: Mon Oct 30 12:59:07 GMT 2023
BAM file: SRX7354223.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): 38,739,783 / 38,712,185
Number of aligned pairs (without duplicates): 38,707,237
Total number of alignments: 82,306,634
Number of secondary alignments: 4,854,666
Number of non-unique alignments: 8,203,238
Aligned to genes: 67,238,165
Ambiguous alignments: 250,829
No feature assigned: 6,333,840
Missing chromosome in annotation: 280,562
Not aligned: 5,575,590

Reads genomic origin

Exonic: 67,238,165 / 91.39%
Intronic: 3,833,122 / 5.21%
Intergenic: 2,500,718 / 3.4%
Intronic/intergenic overlapping exon: 2,511,626 / 3.41%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.21
5'-3' bias: 1.64

Junction analysis

Reads at junctions: 22,673,084
ACCT 5.45%
AGGT 4.74%
ATCT 3.61%
TCCT 3.47%
AGGA 3.36%
GCCT 3.18%
AGCT 2.59%
AGGC 2.41%
TTCT 2.32%
CCCT 2.31%
AGAT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis