Input data and parameters 

Input

Analysis date: Sun Oct 29 12:31:41 GMT 2023
BAM file: SRX7354053.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): 51,044,898 / 50,992,946
Number of aligned pairs (without duplicates): 50,983,671
Total number of alignments: 108,609,243
Number of secondary alignments: 6,571,399
Number of non-unique alignments: 10,895,139
Aligned to genes: 83,032,237
Ambiguous alignments: 311,458
No feature assigned: 13,934,617
Missing chromosome in annotation: 435,792
Not aligned: 11,688,798

Reads genomic origin

Exonic: 83,032,237 / 85.63%
Intronic: 9,417,872 / 9.71%
Intergenic: 4,516,745 / 4.66%
Intronic/intergenic overlapping exon: 3,492,583 / 3.6%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.19
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 25,645,879
ACCT 5.32%
AGGT 4.78%
AGGA 3.58%
TCCT 3.56%
ATCT 3.53%
GCCT 2.95%
AGCT 2.65%
CCCT 2.4%
AGGC 2.38%
AGAT 2.31%
TTCT 2.31%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis