Input data and parameters 

Input

Analysis date: Mon Oct 30 12:43:08 GMT 2023
BAM file: SRX7354213.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): 28,048,816 / 28,021,102
Number of aligned pairs (without duplicates): 28,017,984
Total number of alignments: 59,352,689
Number of secondary alignments: 3,282,771
Number of non-unique alignments: 5,465,685
Aligned to genes: 47,217,192
Ambiguous alignments: 147,918
No feature assigned: 6,316,598
Missing chromosome in annotation: 205,296
Not aligned: 8,007,288

Reads genomic origin

Exonic: 47,217,192 / 88.2%
Intronic: 4,011,286 / 7.49%
Intergenic: 2,305,312 / 4.31%
Intronic/intergenic overlapping exon: 1,813,484 / 3.39%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.16
5'-3' bias: 2.22

Junction analysis

Reads at junctions: 16,740,286
ACCT 5.21%
AGGT 5.07%
AGGA 3.72%
ATCT 3.7%
TCCT 3.42%
AGCT 2.82%
GCCT 2.77%
AGGC 2.48%
CCCT 2.38%
AGAT 2.24%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis