Input data and parameters 

Input

Analysis date: Mon Oct 30 23:00:20 GMT 2023
BAM file: SRX7354268.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): 45,214,002 / 45,187,637
Number of aligned pairs (without duplicates): 45,177,618
Total number of alignments: 97,759,854
Number of secondary alignments: 7,358,215
Number of non-unique alignments: 11,464,691
Aligned to genes: 77,796,320
Ambiguous alignments: 363,721
No feature assigned: 7,356,290
Missing chromosome in annotation: 778,832
Not aligned: 3,522,613

Reads genomic origin

Exonic: 77,796,320 / 91.36%
Intronic: 4,482,980 / 5.26%
Intergenic: 2,873,310 / 3.37%
Intronic/intergenic overlapping exon: 3,633,591 / 4.27%

Transcript coverage profile

5' bias: 0.12
3' bias: 0.11
5'-3' bias: 2.47

Junction analysis

Reads at junctions: 27,231,485
ACCT 5.11%
TCCT 4.77%
AGGT 4.66%
ATCT 4.37%
AGGA 3%
CCCT 2.89%
AGGC 2.65%
GCCT 2.11%
AGAC 2.07%
AGCT 2.02%
AGAA 1.72%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis