Input data and parameters 

Input

Analysis date: Mon Oct 30 20:12:59 GMT 2023
BAM file: SRX7354214.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): 38,645,621 / 38,633,136
Number of aligned pairs (without duplicates): 38,630,238
Total number of alignments: 82,519,718
Number of secondary alignments: 5,240,961
Number of non-unique alignments: 8,492,067
Aligned to genes: 65,131,153
Ambiguous alignments: 205,688
No feature assigned: 8,281,375
Missing chromosome in annotation: 409,435
Not aligned: 910,395

Reads genomic origin

Exonic: 65,131,153 / 88.72%
Intronic: 5,993,149 / 8.16%
Intergenic: 2,288,226 / 3.12%
Intronic/intergenic overlapping exon: 2,199,483 / 3%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.17
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 22,694,642
ACCT 5.06%
AGGT 4.99%
AGGA 3.94%
TCCT 3.68%
ATCT 3.43%
AGCT 2.95%
GCCT 2.43%
AGAT 2.35%
AGGC 2.35%
CCCT 2.21%
TTCT 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