Input data and parameters 

Input

Analysis date: Tue Oct 31 09:55:17 GMT 2023
BAM file: SRX7354411.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): 36,469,457 / 36,447,898
Number of aligned pairs (without duplicates): 36,443,652
Total number of alignments: 77,026,752
Number of secondary alignments: 4,109,397
Number of non-unique alignments: 6,722,927
Aligned to genes: 60,459,420
Ambiguous alignments: 215,088
No feature assigned: 9,307,519
Missing chromosome in annotation: 321,798
Not aligned: 3,068,627

Reads genomic origin

Exonic: 60,459,420 / 86.66%
Intronic: 6,604,193 / 9.47%
Intergenic: 2,703,326 / 3.87%
Intronic/intergenic overlapping exon: 2,522,699 / 3.62%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.2
5'-3' bias: 1.71

Junction analysis

Reads at junctions: 19,423,659
ACCT 5.35%
AGGT 4.66%
ATCT 3.6%
AGGA 3.58%
TCCT 3.38%
GCCT 3.22%
AGCT 2.76%
CCCT 2.37%
AGGC 2.32%
AGAT 2.26%
TTCT 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis