Input data and parameters 

Input

Analysis date: Mon Oct 30 11:09:52 GMT 2023
BAM file: SRX7354219.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): 35,843,790 / 35,808,883
Number of aligned pairs (without duplicates): 35,806,050
Total number of alignments: 76,160,667
Number of secondary alignments: 4,507,994
Number of non-unique alignments: 7,803,299
Aligned to genes: 60,317,768
Ambiguous alignments: 154,636
No feature assigned: 7,645,883
Missing chromosome in annotation: 239,081
Not aligned: 4,645,325

Reads genomic origin

Exonic: 60,317,768 / 88.75%
Intronic: 3,749,416 / 5.52%
Intergenic: 3,896,467 / 5.73%
Intronic/intergenic overlapping exon: 2,256,248 / 3.32%

Transcript coverage profile

5' bias: 0.19
3' bias: 0.09
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 15,952,093
ACCT 4.87%
AGGT 4.66%
AGGA 3.77%
ATCT 3.7%
TCCT 3.34%
AGCT 2.8%
GCCT 2.76%
AGAT 2.59%
TTCT 2.39%
AGGC 2.34%
CCCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis