Input data and parameters 

Input

Analysis date: Sun Oct 29 01:40:01 GMT 2023
BAM file: SRX7354171.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): 27,293,282 / 27,267,676
Number of aligned pairs (without duplicates): 27,263,053
Total number of alignments: 58,166,001
Number of secondary alignments: 3,605,043
Number of non-unique alignments: 5,893,126
Aligned to genes: 46,193,349
Ambiguous alignments: 170,118
No feature assigned: 5,617,542
Missing chromosome in annotation: 291,866
Not aligned: 5,049,338

Reads genomic origin

Exonic: 46,193,349 / 89.16%
Intronic: 2,905,566 / 5.61%
Intergenic: 2,711,976 / 5.23%
Intronic/intergenic overlapping exon: 1,943,327 / 3.75%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.21
5'-3' bias: 1.74

Junction analysis

Reads at junctions: 15,887,057
ACCT 6.04%
ATCT 4.38%
TCCT 4.32%
AGGT 4.23%
GCCT 3.79%
AGGA 2.87%
CCCT 2.77%
TTCT 2.32%
TCCC 2.31%
AGCT 2.16%
AGGC 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis