Input data and parameters 

Input

Analysis date: Tue Oct 31 01:15:00 GMT 2023
BAM file: SRX7354252.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): 35,471,962 / 35,452,961
Number of aligned pairs (without duplicates): 35,448,832
Total number of alignments: 75,473,531
Number of secondary alignments: 4,548,608
Number of non-unique alignments: 6,852,702
Aligned to genes: 59,821,288
Ambiguous alignments: 230,140
No feature assigned: 7,929,610
Missing chromosome in annotation: 639,791
Not aligned: 1,912,663

Reads genomic origin

Exonic: 59,821,288 / 88.3%
Intronic: 5,414,463 / 7.99%
Intergenic: 2,515,147 / 3.71%
Intronic/intergenic overlapping exon: 2,360,782 / 3.48%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.19
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 21,408,486
ACCT 5.57%
AGGT 4.71%
ATCT 3.55%
AGGA 3.5%
TCCT 3.47%
GCCT 3.32%
AGCT 2.63%
CCCT 2.37%
AGGC 2.37%
AGAT 2.17%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis