Input data and parameters 

Input

Analysis date: Mon Oct 30 20:14:52 GMT 2023
BAM file: SRX7354195.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): 46,433,556 / 46,396,691
Number of aligned pairs (without duplicates): 46,384,014
Total number of alignments: 99,423,538
Number of secondary alignments: 6,593,291
Number of non-unique alignments: 10,511,485
Aligned to genes: 79,160,797
Ambiguous alignments: 285,822
No feature assigned: 8,829,560
Missing chromosome in annotation: 635,874
Not aligned: 3,948,711

Reads genomic origin

Exonic: 79,160,797 / 89.97%
Intronic: 5,443,469 / 6.19%
Intergenic: 3,386,091 / 3.85%
Intronic/intergenic overlapping exon: 3,464,192 / 3.94%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.18
5'-3' bias: 2.09

Junction analysis

Reads at junctions: 25,141,832
ACCT 5.38%
AGGT 4.69%
TCCT 3.95%
ATCT 3.79%
AGGA 3.37%
GCCT 2.95%
CCCT 2.52%
AGCT 2.38%
AGGC 2.3%
TTCT 2.04%
AGAT 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis