Input data and parameters 

Input

Analysis date: Mon Oct 30 22:42:56 GMT 2023
BAM file: SRX7354250.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): 40,119,530 / 40,095,269
Number of aligned pairs (without duplicates): 40,091,153
Total number of alignments: 85,136,767
Number of secondary alignments: 4,921,968
Number of non-unique alignments: 7,899,604
Aligned to genes: 66,538,643
Ambiguous alignments: 272,396
No feature assigned: 9,935,478
Missing chromosome in annotation: 490,646
Not aligned: 3,188,711

Reads genomic origin

Exonic: 66,538,643 / 87.01%
Intronic: 5,955,768 / 7.79%
Intergenic: 3,979,710 / 5.2%
Intronic/intergenic overlapping exon: 3,002,008 / 3.93%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.31
5'-3' bias: 1.61

Junction analysis

Reads at junctions: 24,181,798
ACCT 5.12%
AGGT 4.71%
ATCT 3.62%
TCCT 3.6%
GCCT 3.43%
AGGA 3.26%
CCCT 2.68%
AGCT 2.65%
AGGC 2.48%
TTCT 2.41%
AGAT 1.92%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis