Input data and parameters 

Input

Analysis date: Sun Oct 29 01:21:28 GMT 2023
BAM file: SRX7354148.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): 28,838,728 / 28,820,203
Number of aligned pairs (without duplicates): 28,816,820
Total number of alignments: 61,366,141
Number of secondary alignments: 3,707,210
Number of non-unique alignments: 6,039,514
Aligned to genes: 47,425,420
Ambiguous alignments: 151,426
No feature assigned: 7,417,694
Missing chromosome in annotation: 332,087
Not aligned: 3,004,879

Reads genomic origin

Exonic: 47,425,420 / 86.47%
Intronic: 5,020,951 / 9.16%
Intergenic: 2,396,743 / 4.37%
Intronic/intergenic overlapping exon: 1,863,526 / 3.4%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.21
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 15,923,729
ACCT 5.27%
AGGT 4.82%
ATCT 3.8%
AGGA 3.63%
TCCT 3.46%
GCCT 2.9%
AGCT 2.85%
AGGC 2.38%
CCCT 2.38%
AGAT 2.33%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis