Input data and parameters 

Input

Analysis date: Tue Oct 31 10:04:10 GMT 2023
BAM file: SRX7354331.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): 57,922,780 / 57,795,728
Number of aligned pairs (without duplicates): 57,781,796
Total number of alignments: 122,855,076
Number of secondary alignments: 7,136,568
Number of non-unique alignments: 11,349,271
Aligned to genes: 92,481,700
Ambiguous alignments: 356,800
No feature assigned: 17,946,866
Missing chromosome in annotation: 720,439
Not aligned: 27,840,528

Reads genomic origin

Exonic: 92,481,700 / 83.75%
Intronic: 12,154,731 / 11.01%
Intergenic: 5,792,135 / 5.25%
Intronic/intergenic overlapping exon: 4,570,860 / 4.14%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.3
5'-3' bias: 1.65

Junction analysis

Reads at junctions: 39,181,914
ACCT 5.15%
AGGT 4.73%
TCCT 3.7%
ATCT 3.52%
AGGA 3.37%
GCCT 3.28%
AGCT 2.77%
CCCT 2.75%
AGGC 2.51%
AGAT 2.04%
TTCT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis