Input data and parameters 

Input

Analysis date: Tue Oct 31 01:31:28 GMT 2023
BAM file: SRX7354315.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): 50,541,327 / 50,501,007
Number of aligned pairs (without duplicates): 50,496,485
Total number of alignments: 107,373,695
Number of secondary alignments: 6,331,361
Number of non-unique alignments: 10,718,986
Aligned to genes: 87,240,060
Ambiguous alignments: 258,539
No feature assigned: 8,719,573
Missing chromosome in annotation: 436,537
Not aligned: 4,942,102

Reads genomic origin

Exonic: 87,240,060 / 90.91%
Intronic: 4,484,289 / 4.67%
Intergenic: 4,235,284 / 4.41%
Intronic/intergenic overlapping exon: 3,319,745 / 3.46%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.17
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 26,824,098
ACCT 5.27%
AGGT 4.64%
ATCT 3.55%
AGGA 3.55%
TCCT 3.35%
GCCT 3.14%
AGCT 2.79%
AGGC 2.38%
TTCT 2.28%
AGAT 2.26%
CCCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis