Input data and parameters 

Input

Analysis date: Sun Oct 29 01:57:44 GMT 2023
BAM file: SRX7354099.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): 32,739,446 / 32,707,132
Number of aligned pairs (without duplicates): 32,701,198
Total number of alignments: 69,858,176
Number of secondary alignments: 4,411,598
Number of non-unique alignments: 6,989,813
Aligned to genes: 56,402,585
Ambiguous alignments: 215,522
No feature assigned: 5,862,154
Missing chromosome in annotation: 388,102
Not aligned: 4,158,452

Reads genomic origin

Exonic: 56,402,585 / 90.59%
Intronic: 3,593,741 / 5.77%
Intergenic: 2,268,413 / 3.64%
Intronic/intergenic overlapping exon: 2,195,794 / 3.53%

Transcript coverage profile

5' bias: 0.13
3' bias: 0.16
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 17,886,348
ATCT 5.08%
ACCT 4.81%
TCCT 4.62%
AGGT 4.48%
CCCT 3.55%
AGGA 3.04%
GCCT 2.62%
TTCT 2.42%
AGCT 2.12%
AGGC 2.08%
AGAA 1.96%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis