Input data and parameters 

Input

Analysis date: Mon Oct 30 22:50:50 GMT 2023
BAM file: SRX7354224.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): 47,798,095 / 47,763,019
Number of aligned pairs (without duplicates): 47,740,269
Total number of alignments: 102,482,624
Number of secondary alignments: 6,921,510
Number of non-unique alignments: 11,496,742
Aligned to genes: 79,276,531
Ambiguous alignments: 295,038
No feature assigned: 10,879,073
Missing chromosome in annotation: 535,240
Not aligned: 1,311,686

Reads genomic origin

Exonic: 79,276,531 / 87.93%
Intronic: 8,138,793 / 9.03%
Intergenic: 2,740,280 / 3.04%
Intronic/intergenic overlapping exon: 3,862,876 / 4.28%

Transcript coverage profile

5' bias: 0.53
3' bias: 0.19
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 31,681,594
ACCT 5.15%
AGGT 4.85%
AGGA 3.57%
ATCT 3.35%
TCCT 3.27%
AGCT 2.87%
GCCT 2.82%
AGGC 2.47%
CCCT 2.44%
AGAT 2.2%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis