Input data and parameters 

Input

Analysis date: Tue Oct 31 09:59:17 GMT 2023
BAM file: SRX7354353.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): 34,792,685 / 34,780,285
Number of aligned pairs (without duplicates): 34,777,503
Total number of alignments: 74,629,900
Number of secondary alignments: 5,056,930
Number of non-unique alignments: 8,265,686
Aligned to genes: 54,592,633
Ambiguous alignments: 200,522
No feature assigned: 11,193,028
Missing chromosome in annotation: 378,031
Not aligned: 2,305,876

Reads genomic origin

Exonic: 54,592,633 / 82.99%
Intronic: 6,925,938 / 10.53%
Intergenic: 4,267,090 / 6.49%
Intronic/intergenic overlapping exon: 2,187,974 / 3.33%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.26
5'-3' bias: 1.65

Junction analysis

Reads at junctions: 19,035,250
ACCT 5.21%
AGGT 4.77%
ATCT 3.57%
TCCT 3.51%
AGGA 3.46%
GCCT 3.13%
AGCT 2.64%
CCCT 2.56%
AGGC 2.43%
TTCT 2.29%
AGAT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis