Input data and parameters 

Input

Analysis date: Mon Oct 30 11:28:41 GMT 2023
BAM file: SRX7354199.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): 68,191,728 / 68,112,484
Number of aligned pairs (without duplicates): 68,089,603
Total number of alignments: 149,085,688
Number of secondary alignments: 12,781,476
Number of non-unique alignments: 19,188,447
Aligned to genes: 116,356,982
Ambiguous alignments: 499,705
No feature assigned: 11,132,710
Missing chromosome in annotation: 1,907,844
Not aligned: 11,338,136

Reads genomic origin

Exonic: 116,356,982 / 91.27%
Intronic: 5,748,148 / 4.51%
Intergenic: 5,384,562 / 4.22%
Intronic/intergenic overlapping exon: 5,103,313 / 4%

Transcript coverage profile

5' bias: 0.14
3' bias: 0.14
5'-3' bias: 2.26

Junction analysis

Reads at junctions: 37,028,457
TCCT 4.71%
ACCT 4.57%
AGGT 4.49%
ATCT 4.36%
CCCT 3.88%
AGGA 3.15%
AGGC 2.55%
AGAC 2.41%
GCCT 2.14%
AGCT 2.1%
GTCT 1.95%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis