Input data and parameters 

Input

Analysis date: Tue Oct 31 09:56:55 GMT 2023
BAM file: SRX7354325.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): 59,848,435 / 59,804,695
Number of aligned pairs (without duplicates): 59,794,158
Total number of alignments: 129,845,037
Number of secondary alignments: 10,191,907
Number of non-unique alignments: 15,790,042
Aligned to genes: 100,950,740
Ambiguous alignments: 414,973
No feature assigned: 11,588,553
Missing chromosome in annotation: 1,100,729
Not aligned: 7,798,324

Reads genomic origin

Exonic: 100,950,740 / 89.7%
Intronic: 6,257,046 / 5.56%
Intergenic: 5,331,507 / 4.74%
Intronic/intergenic overlapping exon: 4,848,282 / 4.31%

Transcript coverage profile

5' bias: 0.05
3' bias: 0.07
5'-3' bias: 2.8

Junction analysis

Reads at junctions: 32,715,761
TCCT 5.61%
ACCT 4.9%
AGGT 4.37%
ATCT 4.18%
CCCT 3.93%
AGGA 3.29%
AGGC 2.08%
TGCT 1.98%
AGAC 1.93%
AGCT 1.83%
GTCT 1.83%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis