Input data and parameters 

Input

Analysis date: Tue Oct 31 01:12:27 GMT 2023
BAM file: SRX7354334.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): 34,181,836 / 34,128,589
Number of aligned pairs (without duplicates): 34,122,885
Total number of alignments: 82,606,174
Number of secondary alignments: 14,295,749
Number of non-unique alignments: 13,212,734
Aligned to genes: 52,160,391
Ambiguous alignments: 226,639
No feature assigned: 11,033,299
Missing chromosome in annotation: 5,973,111
Not aligned: 8,477,015

Reads genomic origin

Exonic: 52,160,391 / 82.54%
Intronic: 6,898,587 / 10.92%
Intergenic: 4,134,712 / 6.54%
Intronic/intergenic overlapping exon: 2,401,829 / 3.8%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.35
5'-3' bias: 1.66

Junction analysis

Reads at junctions: 20,706,194
ACCT 5.41%
AGGT 4.55%
TCCT 3.84%
ATCT 3.52%
GCCT 3.44%
AGGA 3.17%
CCCT 2.82%
AGCT 2.52%
AGGC 2.42%
TTCT 2.15%
AGAT 2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis