Input data and parameters 

Input

Analysis date: Tue Oct 31 09:22:42 GMT 2023
BAM file: SRX7354277.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): 50,223,727 / 50,181,474
Number of aligned pairs (without duplicates): 50,162,522
Total number of alignments: 107,944,856
Number of secondary alignments: 7,539,655
Number of non-unique alignments: 12,629,491
Aligned to genes: 80,107,205
Ambiguous alignments: 286,846
No feature assigned: 14,445,370
Missing chromosome in annotation: 475,944
Not aligned: 5,527,373

Reads genomic origin

Exonic: 80,107,205 / 84.72%
Intronic: 10,571,629 / 11.18%
Intergenic: 3,873,741 / 4.1%
Intronic/intergenic overlapping exon: 4,344,347 / 4.59%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.13
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 26,480,840
ACCT 5.32%
AGGT 4.71%
AGGA 3.61%
ATCT 3.53%
TCCT 3.31%
GCCT 3.27%
AGCT 2.77%
AGAT 2.35%
CCCT 2.34%
AGGC 2.33%
TTCT 2.26%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis