Input data and parameters 

Input

Analysis date: Sun Oct 29 01:56:52 GMT 2023
BAM file: SRX7354096.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): 55,529,928 / 55,490,400
Number of aligned pairs (without duplicates): 55,484,401
Total number of alignments: 119,426,315
Number of secondary alignments: 8,405,987
Number of non-unique alignments: 13,986,788
Aligned to genes: 92,240,458
Ambiguous alignments: 319,090
No feature assigned: 12,300,535
Missing chromosome in annotation: 579,444
Not aligned: 5,226,298

Reads genomic origin

Exonic: 92,240,458 / 88.23%
Intronic: 6,870,606 / 6.57%
Intergenic: 5,429,929 / 5.19%
Intronic/intergenic overlapping exon: 3,443,769 / 3.29%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.2
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 29,007,850
ACCT 5.26%
AGGT 4.91%
AGGA 3.65%
TCCT 3.64%
ATCT 3.52%
GCCT 2.73%
AGCT 2.68%
CCCT 2.53%
AGGC 2.41%
TTCT 2.25%
AGAT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis