Input data and parameters 

Input

Analysis date: Tue Oct 31 10:15:13 GMT 2023
BAM file: SRX7354348.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): 72,536,996 / 72,475,033
Number of aligned pairs (without duplicates): 72,468,922
Total number of alignments: 154,136,693
Number of secondary alignments: 9,124,664
Number of non-unique alignments: 15,150,620
Aligned to genes: 122,359,663
Ambiguous alignments: 377,440
No feature assigned: 15,540,563
Missing chromosome in annotation: 708,407
Not aligned: 10,643,469

Reads genomic origin

Exonic: 122,359,663 / 88.73%
Intronic: 9,386,149 / 6.81%
Intergenic: 6,154,414 / 4.46%
Intronic/intergenic overlapping exon: 4,630,179 / 3.36%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.15
5'-3' bias: 2

Junction analysis

Reads at junctions: 37,620,799
ACCT 5.35%
AGGT 4.72%
ATCT 3.86%
AGGA 3.63%
TCCT 3.37%
GCCT 3.26%
AGCT 2.72%
CCCT 2.43%
AGGC 2.38%
AGAT 2.26%
TTCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis