Input data and parameters 

Input

Analysis date: Mon Oct 30 09:53:57 GMT 2023
BAM file: SRX7354104.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): 72,100,340 / 72,056,285
Number of aligned pairs (without duplicates): 72,045,443
Total number of alignments: 155,246,628
Number of secondary alignments: 11,090,003
Number of non-unique alignments: 17,401,762
Aligned to genes: 126,436,936
Ambiguous alignments: 504,321
No feature assigned: 9,825,470
Missing chromosome in annotation: 1,078,139
Not aligned: 5,082,159

Reads genomic origin

Exonic: 126,436,936 / 92.79%
Intronic: 6,367,878 / 4.67%
Intergenic: 3,457,592 / 2.54%
Intronic/intergenic overlapping exon: 4,977,528 / 3.65%

Transcript coverage profile

5' bias: 0.19
3' bias: 0.18
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 53,325,136
ACCT 5.42%
TCCT 4.9%
AGGT 4.63%
ATCT 4.35%
AGGA 3.11%
CCCT 2.73%
GCCT 2.68%
AGGC 2.19%
AGCT 2.1%
TTCT 2.02%
AGAA 1.91%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis