Input data and parameters 

Input

Analysis date: Tue Oct 31 12:08:44 GMT 2023
BAM file: SRX7354363.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): 34,741,126 / 34,709,660
Number of aligned pairs (without duplicates): 34,704,178
Total number of alignments: 74,030,807
Number of secondary alignments: 4,580,021
Number of non-unique alignments: 7,514,933
Aligned to genes: 57,238,542
Ambiguous alignments: 191,903
No feature assigned: 8,707,180
Missing chromosome in annotation: 378,249
Not aligned: 4,389,570

Reads genomic origin

Exonic: 57,238,542 / 86.8%
Intronic: 5,554,891 / 8.42%
Intergenic: 3,152,289 / 4.78%
Intronic/intergenic overlapping exon: 2,179,623 / 3.31%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.2
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 16,977,865
ACCT 5.57%
AGGT 4.66%
ATCT 3.56%
AGGA 3.53%
TCCT 3.42%
GCCT 3.34%
AGCT 2.67%
CCCT 2.48%
AGGC 2.34%
AGAT 2.23%
TTCT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis