Input data and parameters 

Input

Analysis date: Mon Oct 30 09:28:48 GMT 2023
BAM file: SRX7354154.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): 43,958,974 / 43,931,656
Number of aligned pairs (without duplicates): 43,920,759
Total number of alignments: 95,778,872
Number of secondary alignments: 7,888,242
Number of non-unique alignments: 11,971,165
Aligned to genes: 74,402,360
Ambiguous alignments: 323,932
No feature assigned: 8,028,480
Missing chromosome in annotation: 1,052,935
Not aligned: 2,309,888

Reads genomic origin

Exonic: 74,402,360 / 90.26%
Intronic: 4,889,934 / 5.93%
Intergenic: 3,138,546 / 3.81%
Intronic/intergenic overlapping exon: 3,715,801 / 4.51%

Transcript coverage profile

5' bias: 0.14
3' bias: 0.14
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 23,854,712
TCCT 5.58%
ACCT 5.09%
ATCT 4.87%
AGGT 4.21%
CCCT 3.35%
AGGA 2.96%
GCCT 2.57%
TTCT 2.4%
AGGC 2.14%
AGCT 1.99%
GTCT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis