Input data and parameters 

Input

Analysis date: Tue Oct 31 09:58:55 GMT 2023
BAM file: SRX7354373.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): 44,530,709 / 44,460,156
Number of aligned pairs (without duplicates): 44,455,117
Total number of alignments: 95,735,349
Number of secondary alignments: 6,744,484
Number of non-unique alignments: 10,579,769
Aligned to genes: 71,136,528
Ambiguous alignments: 262,281
No feature assigned: 12,978,644
Missing chromosome in annotation: 778,127
Not aligned: 7,438,063

Reads genomic origin

Exonic: 71,136,528 / 84.57%
Intronic: 7,488,293 / 8.9%
Intergenic: 5,490,351 / 6.53%
Intronic/intergenic overlapping exon: 2,904,588 / 3.45%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.37
5'-3' bias: 1.67

Junction analysis

Reads at junctions: 26,188,065
ACCT 5.31%
AGGT 4.5%
TCCT 3.96%
ATCT 3.64%
GCCT 3.35%
AGGA 3.28%
CCCT 2.79%
AGCT 2.68%
AGGC 2.38%
TTCT 2.15%
AGAT 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis