Input data and parameters 

Input

Analysis date: Sun Oct 29 01:44:25 GMT 2023
BAM file: SRX7354183.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): 36,392,574 / 36,380,480
Number of aligned pairs (without duplicates): 36,377,388
Total number of alignments: 78,111,554
Number of secondary alignments: 5,338,500
Number of non-unique alignments: 8,483,075
Aligned to genes: 57,184,622
Ambiguous alignments: 222,862
No feature assigned: 11,639,800
Missing chromosome in annotation: 581,195
Not aligned: 1,949,258

Reads genomic origin

Exonic: 57,184,622 / 83.09%
Intronic: 7,322,000 / 10.64%
Intergenic: 4,317,800 / 6.27%
Intronic/intergenic overlapping exon: 2,388,646 / 3.47%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.3
5'-3' bias: 1.63

Junction analysis

Reads at junctions: 21,481,595
ACCT 5.18%
AGGT 4.67%
ATCT 3.61%
TCCT 3.49%
GCCT 3.47%
AGGA 3.36%
AGCT 2.76%
CCCT 2.73%
AGGC 2.43%
TTCT 2.19%
AGAT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis