Input data and parameters 

Input

Analysis date: Tue Oct 31 09:58:09 GMT 2023
BAM file: SRX7354345.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): 48,340,633 / 48,272,027
Number of aligned pairs (without duplicates): 48,264,211
Total number of alignments: 103,230,966
Number of secondary alignments: 6,618,306
Number of non-unique alignments: 10,552,453
Aligned to genes: 75,749,067
Ambiguous alignments: 308,048
No feature assigned: 16,181,452
Missing chromosome in annotation: 439,946
Not aligned: 8,794,340

Reads genomic origin

Exonic: 75,749,067 / 82.4%
Intronic: 12,716,535 / 13.83%
Intergenic: 3,464,917 / 3.77%
Intronic/intergenic overlapping exon: 3,208,859 / 3.49%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.16
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 26,687,230
ACCT 5.53%
AGGT 4.75%
AGGA 3.66%
ATCT 3.5%
TCCT 3.47%
AGCT 2.69%
GCCT 2.64%
TTCT 2.45%
AGAT 2.45%
AGGC 2.33%
CCCT 2.31%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis