Input data and parameters 

Input

Analysis date: Mon Oct 30 09:23:48 GMT 2023
BAM file: SRX7354156.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): 31,285,813 / 31,266,266
Number of aligned pairs (without duplicates): 31,263,886
Total number of alignments: 66,202,406
Number of secondary alignments: 3,650,327
Number of non-unique alignments: 6,012,280
Aligned to genes: 51,603,353
Ambiguous alignments: 171,049
No feature assigned: 8,137,511
Missing chromosome in annotation: 278,213
Not aligned: 1,318,855

Reads genomic origin

Exonic: 51,603,353 / 86.38%
Intronic: 5,672,063 / 9.49%
Intergenic: 2,465,448 / 4.13%
Intronic/intergenic overlapping exon: 1,982,629 / 3.32%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.16
5'-3' bias: 2.24

Junction analysis

Reads at junctions: 16,710,064
ACCT 5.37%
AGGT 4.69%
AGGA 3.63%
ATCT 3.63%
TCCT 3.37%
GCCT 3.1%
AGCT 2.74%
AGGC 2.42%
AGAT 2.4%
CCCT 2.38%
TTCT 2.26%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis