Input data and parameters 

Input

Analysis date: Mon Oct 30 09:47:06 GMT 2023
BAM file: SRX7354187.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): 48,712,103 / 48,648,376
Number of aligned pairs (without duplicates): 48,626,652
Total number of alignments: 112,351,257
Number of secondary alignments: 14,990,778
Number of non-unique alignments: 17,645,355
Aligned to genes: 79,739,866
Ambiguous alignments: 342,960
No feature assigned: 10,013,261
Missing chromosome in annotation: 4,609,815
Not aligned: 2,921,695

Reads genomic origin

Exonic: 79,739,866 / 88.84%
Intronic: 6,707,396 / 7.47%
Intergenic: 3,305,865 / 3.68%
Intronic/intergenic overlapping exon: 4,575,031 / 5.1%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.26
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 30,252,804
ACCT 5.66%
AGGT 4.37%
TCCT 4.04%
ATCT 3.74%
GCCT 3.51%
AGGA 3.15%
CCCT 2.78%
AGCT 2.61%
AGGC 2.34%
TTCT 2.21%
TCCC 1.86%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis