Input data and parameters 

Input

Analysis date: Tue Oct 31 16:17:23 GMT 2023
BAM file: SRX7354397.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): 120,988,440 / 120,784,066
Number of aligned pairs (without duplicates): 120,756,260
Total number of alignments: 260,955,046
Number of secondary alignments: 19,182,540
Number of non-unique alignments: 32,320,132
Aligned to genes: 197,286,625
Ambiguous alignments: 678,304
No feature assigned: 29,208,659
Missing chromosome in annotation: 1,461,326
Not aligned: 11,959,526

Reads genomic origin

Exonic: 197,286,625 / 87.1%
Intronic: 19,977,517 / 8.82%
Intergenic: 9,231,142 / 4.08%
Intronic/intergenic overlapping exon: 11,024,286 / 4.87%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.25
5'-3' bias: 1.68

Junction analysis

Reads at junctions: 65,274,198
ACCT 5.05%
AGGT 4.58%
TCCT 3.81%
ATCT 3.74%
GCCT 3.57%
AGGA 3.21%
CCCT 2.76%
AGCT 2.73%
AGGC 2.4%
TTCT 2.3%
AGAT 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