Input data and parameters 

Input

Analysis date: Sun Oct 29 11:43:18 GMT 2023
BAM file: SRX7354089.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): 39,245,384 / 39,207,108
Number of aligned pairs (without duplicates): 39,202,588
Total number of alignments: 83,230,503
Number of secondary alignments: 4,778,011
Number of non-unique alignments: 8,038,896
Aligned to genes: 65,922,604
Ambiguous alignments: 206,603
No feature assigned: 8,718,287
Missing chromosome in annotation: 344,113
Not aligned: 8,364,196

Reads genomic origin

Exonic: 65,922,604 / 88.32%
Intronic: 5,360,025 / 7.18%
Intergenic: 3,358,262 / 4.5%
Intronic/intergenic overlapping exon: 2,750,948 / 3.69%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.18
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 19,881,417
ACCT 5.26%
AGGT 4.68%
ATCT 4.07%
TCCT 3.51%
AGGA 3.45%
GCCT 3.22%
AGCT 2.61%
CCCT 2.54%
AGGC 2.34%
TTCT 2.2%
AGAT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis