Input data and parameters 

Input

Analysis date: Tue Oct 31 10:06:53 GMT 2023
BAM file: SRX7354362.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): 43,978,881 / 43,919,166
Number of aligned pairs (without duplicates): 43,886,241
Total number of alignments: 95,586,212
Number of secondary alignments: 7,688,165
Number of non-unique alignments: 12,424,656
Aligned to genes: 75,155,826
Ambiguous alignments: 322,107
No feature assigned: 7,228,997
Missing chromosome in annotation: 454,626
Not aligned: 8,659,603

Reads genomic origin

Exonic: 75,155,826 / 91.23%
Intronic: 4,574,525 / 5.55%
Intergenic: 2,654,472 / 3.22%
Intronic/intergenic overlapping exon: 2,726,090 / 3.31%

Transcript coverage profile

5' bias: 0.11
3' bias: 0.13
5'-3' bias: 1.84

Junction analysis

Reads at junctions: 23,923,474
ACCT 5.76%
AGGT 4.71%
TCCT 4.27%
ATCT 3.79%
AGGA 3.33%
CCCT 2.64%
GCCT 2.4%
AGGC 2.23%
AGCT 2.02%
TTCT 1.83%
AGAT 1.79%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis