Input data and parameters 

Input

Analysis date: Tue Oct 31 14:14:08 GMT 2023
BAM file: SRX7354370.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): 36,010,493 / 35,966,609
Number of aligned pairs (without duplicates): 35,945,505
Total number of alignments: 77,885,943
Number of secondary alignments: 5,908,841
Number of non-unique alignments: 9,901,506
Aligned to genes: 60,770,952
Ambiguous alignments: 260,415
No feature assigned: 6,553,372
Missing chromosome in annotation: 399,698
Not aligned: 3,460,168

Reads genomic origin

Exonic: 60,770,952 / 90.27%
Intronic: 3,803,671 / 5.65%
Intergenic: 2,749,701 / 4.08%
Intronic/intergenic overlapping exon: 2,956,712 / 4.39%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.22
5'-3' bias: 2.18

Junction analysis

Reads at junctions: 20,368,782
ACCT 5.5%
TCCT 4.9%
ATCT 4.58%
AGGT 4.16%
CCCT 3.33%
GCCT 3.32%
AGGA 2.84%
TTCT 2.33%
AGCT 2.2%
AGGC 2.18%
TCCC 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis