Input data and parameters 

Input

Analysis date: Tue Oct 31 13:21:54 GMT 2023
BAM file: SRX7354380.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): 32,475,923 / 32,454,361
Number of aligned pairs (without duplicates): 32,450,754
Total number of alignments: 68,982,208
Number of secondary alignments: 4,051,924
Number of non-unique alignments: 6,742,741
Aligned to genes: 54,667,406
Ambiguous alignments: 181,723
No feature assigned: 7,130,079
Missing chromosome in annotation: 260,259
Not aligned: 3,222,682

Reads genomic origin

Exonic: 54,667,406 / 88.46%
Intronic: 4,815,554 / 7.79%
Intergenic: 2,314,525 / 3.75%
Intronic/intergenic overlapping exon: 2,056,989 / 3.33%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.21
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 19,038,012
ACCT 5.25%
AGGT 4.55%
ATCT 3.56%
AGGA 3.52%
TCCT 3.4%
GCCT 3.21%
AGCT 2.88%
AGGC 2.35%
AGAT 2.27%
CCCT 2.26%
TTCT 2.08%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis