Input data and parameters 

Input

Analysis date: Mon Oct 30 13:15:40 GMT 2023
BAM file: SRX7354188.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): 77,171,218 / 77,078,129
Number of aligned pairs (without duplicates): 77,071,324
Total number of alignments: 162,617,416
Number of secondary alignments: 8,368,069
Number of non-unique alignments: 13,913,559
Aligned to genes: 132,003,600
Ambiguous alignments: 377,175
No feature assigned: 15,718,235
Missing chromosome in annotation: 604,847
Not aligned: 6,855,957

Reads genomic origin

Exonic: 132,003,600 / 89.36%
Intronic: 8,476,216 / 5.74%
Intergenic: 7,242,019 / 4.9%
Intronic/intergenic overlapping exon: 5,774,933 / 3.91%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.15
5'-3' bias: 2.2

Junction analysis

Reads at junctions: 45,019,235
ACCT 5.45%
AGGT 4.8%
AGGA 3.57%
ATCT 3.48%
TCCT 3.32%
GCCT 3.1%
AGCT 2.82%
AGGC 2.43%
CCCT 2.26%
AGAT 2.2%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis