Input data and parameters 

Input

Analysis date: Sun Oct 29 11:57:54 GMT 2023
BAM file: SRX7354143.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): 42,420,283 / 42,408,075
Number of aligned pairs (without duplicates): 42,402,310
Total number of alignments: 90,313,194
Number of secondary alignments: 5,484,836
Number of non-unique alignments: 8,866,595
Aligned to genes: 71,504,395
Ambiguous alignments: 229,608
No feature assigned: 9,238,353
Missing chromosome in annotation: 474,243
Not aligned: 1,906,390

Reads genomic origin

Exonic: 71,504,395 / 88.56%
Intronic: 6,590,273 / 8.16%
Intergenic: 2,648,080 / 3.28%
Intronic/intergenic overlapping exon: 3,031,823 / 3.75%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.17
5'-3' bias: 2.21

Junction analysis

Reads at junctions: 24,151,636
ACCT 5.47%
AGGT 4.69%
ATCT 3.79%
TCCT 3.61%
AGGA 3.5%
GCCT 3.16%
AGCT 2.59%
AGGC 2.34%
CCCT 2.31%
AGAT 2.08%
TTCT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis