Input data and parameters 

Input

Analysis date: Sun Oct 29 12:26:23 GMT 2023
BAM file: SRX7354074.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): 91,252,929 / 91,043,857
Number of aligned pairs (without duplicates): 91,027,741
Total number of alignments: 195,027,732
Number of secondary alignments: 12,730,946
Number of non-unique alignments: 20,435,273
Aligned to genes: 145,789,904
Ambiguous alignments: 573,821
No feature assigned: 27,080,025
Missing chromosome in annotation: 1,148,709
Not aligned: 23,316,472

Reads genomic origin

Exonic: 145,789,904 / 84.34%
Intronic: 16,343,125 / 9.45%
Intergenic: 10,736,900 / 6.21%
Intronic/intergenic overlapping exon: 6,816,246 / 3.94%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.32
5'-3' bias: 1.62

Junction analysis

Reads at junctions: 57,521,364
ACCT 5.07%
AGGT 4.7%
TCCT 3.93%
ATCT 3.73%
GCCT 3.28%
AGGA 3.16%
CCCT 2.8%
AGCT 2.56%
AGGC 2.52%
TTCT 2.19%
AGAT 1.89%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis