Input data and parameters 

Input

Analysis date: Mon Oct 30 11:27:10 GMT 2023
BAM file: SRX7354176.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): 54,054,724 / 54,021,877
Number of aligned pairs (without duplicates): 54,017,634
Total number of alignments: 115,095,605
Number of secondary alignments: 7,019,004
Number of non-unique alignments: 11,428,245
Aligned to genes: 89,095,457
Ambiguous alignments: 272,508
No feature assigned: 13,685,732
Missing chromosome in annotation: 613,663
Not aligned: 3,817,363

Reads genomic origin

Exonic: 89,095,457 / 86.68%
Intronic: 8,506,016 / 8.28%
Intergenic: 5,179,716 / 5.04%
Intronic/intergenic overlapping exon: 3,673,528 / 3.57%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.19
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 26,635,579
ACCT 5.43%
AGGT 4.74%
AGGA 3.62%
ATCT 3.59%
TCCT 3.46%
GCCT 3.31%
AGCT 2.62%
AGGC 2.41%
CCCT 2.39%
AGAT 2.25%
TTCT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis