Input data and parameters 

Input

Analysis date: Sun Oct 29 12:32:41 GMT 2023
BAM file: SRX7354174.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): 24,391,287 / 24,369,594
Number of aligned pairs (without duplicates): 24,367,368
Total number of alignments: 52,696,887
Number of secondary alignments: 3,936,006
Number of non-unique alignments: 5,659,039
Aligned to genes: 42,011,593
Ambiguous alignments: 183,673
No feature assigned: 4,177,882
Missing chromosome in annotation: 664,700
Not aligned: 2,150,599

Reads genomic origin

Exonic: 42,011,593 / 90.95%
Intronic: 2,513,010 / 5.44%
Intergenic: 1,664,872 / 3.6%
Intronic/intergenic overlapping exon: 1,470,901 / 3.18%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.22
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 13,987,444
ACCT 5.38%
AGGT 4.7%
ATCT 4.04%
TCCT 3.91%
GCCT 3.25%
AGGA 3.2%
CCCT 2.64%
AGCT 2.37%
TTCT 2.37%
AGGC 2.24%
AGAA 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis