Input data and parameters 

Input

Analysis date: Mon Oct 30 20:29:46 GMT 2023
BAM file: SRX7354196.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): 54,271,593 / 54,200,545
Number of aligned pairs (without duplicates): 54,183,176
Total number of alignments: 115,220,285
Number of secondary alignments: 6,748,147
Number of non-unique alignments: 11,548,081
Aligned to genes: 87,743,121
Ambiguous alignments: 265,878
No feature assigned: 15,315,608
Missing chromosome in annotation: 347,597
Not aligned: 8,087,236

Reads genomic origin

Exonic: 87,743,121 / 85.14%
Intronic: 10,289,725 / 9.98%
Intergenic: 5,025,883 / 4.88%
Intronic/intergenic overlapping exon: 4,251,535 / 4.13%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.17
5'-3' bias: 2.03

Junction analysis

Reads at junctions: 25,064,274
ACCT 5.31%
AGGT 4.81%
AGGA 3.67%
ATCT 3.63%
TCCT 3.34%
GCCT 2.94%
AGCT 2.83%
CCCT 2.43%
AGGC 2.43%
AGAT 2.41%
TTCT 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