Input data and parameters 

Input

Analysis date: Mon Oct 30 22:31:03 GMT 2023
BAM file: SRX7354285.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): 42,783,518 / 42,761,557
Number of aligned pairs (without duplicates): 42,755,426
Total number of alignments: 92,605,346
Number of secondary alignments: 7,060,271
Number of non-unique alignments: 10,411,634
Aligned to genes: 73,515,350
Ambiguous alignments: 346,357
No feature assigned: 7,165,298
Missing chromosome in annotation: 1,166,707
Not aligned: 2,328,623

Reads genomic origin

Exonic: 73,515,350 / 91.12%
Intronic: 3,750,561 / 4.65%
Intergenic: 3,414,737 / 4.23%
Intronic/intergenic overlapping exon: 3,354,341 / 4.16%

Transcript coverage profile

5' bias: 0.14
3' bias: 0.15
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 23,119,113
TCCT 4.94%
ACCT 4.76%
AGGT 4.51%
ATCT 4.39%
CCCT 3.72%
AGGA 3.1%
AGGC 2.33%
GCCT 2.33%
AGCT 2.15%
TTCT 2.07%
GTCT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis