Input data and parameters 

Input

Analysis date: Tue Oct 31 09:33:22 GMT 2023
BAM file: SRX7354301.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): 48,518,338 / 48,502,337
Number of aligned pairs (without duplicates): 48,480,640
Total number of alignments: 107,131,429
Number of secondary alignments: 10,110,754
Number of non-unique alignments: 15,805,132
Aligned to genes: 81,848,094
Ambiguous alignments: 349,132
No feature assigned: 8,188,585
Missing chromosome in annotation: 940,486
Not aligned: 4,383,679

Reads genomic origin

Exonic: 81,848,094 / 90.91%
Intronic: 4,629,773 / 5.14%
Intergenic: 3,558,812 / 3.95%
Intronic/intergenic overlapping exon: 4,204,894 / 4.67%

Transcript coverage profile

5' bias: 0.09
3' bias: 0.12
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 25,541,965
TCCT 5.68%
ACCT 5.68%
ATCT 4.68%
AGGT 4%
CCCT 3.64%
AGGA 2.78%
GCCT 2.43%
AGGC 2.28%
TCCC 2.24%
TTCT 2.01%
CGTA 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis