Input data and parameters 

Input

Analysis date: Tue Oct 31 09:52:50 GMT 2023
BAM file: SRX7354372.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): 27,369,383 / 27,351,515
Number of aligned pairs (without duplicates): 27,348,120
Total number of alignments: 58,297,497
Number of secondary alignments: 3,576,599
Number of non-unique alignments: 5,918,889
Aligned to genes: 46,010,813
Ambiguous alignments: 166,217
No feature assigned: 5,946,610
Missing chromosome in annotation: 254,968
Not aligned: 1,856,902

Reads genomic origin

Exonic: 46,010,813 / 88.55%
Intronic: 3,901,775 / 7.51%
Intergenic: 2,044,835 / 3.94%
Intronic/intergenic overlapping exon: 1,704,629 / 3.28%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.2
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 13,551,106
ACCT 5.23%
AGGT 4.67%
ATCT 3.73%
TCCT 3.61%
AGGA 3.54%
GCCT 3.03%
AGCT 2.62%
CCCT 2.54%
AGGC 2.34%
TTCT 2.28%
AGAT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis