Input data and parameters 

Input

Analysis date: Sun Oct 29 02:21:23 GMT 2023
BAM file: SRX7354149.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): 50,378,992 / 50,325,321
Number of aligned pairs (without duplicates): 50,301,081
Total number of alignments: 107,191,100
Number of secondary alignments: 6,486,787
Number of non-unique alignments: 10,447,453
Aligned to genes: 84,572,405
Ambiguous alignments: 332,673
No feature assigned: 11,253,456
Missing chromosome in annotation: 585,113
Not aligned: 2,223,511

Reads genomic origin

Exonic: 84,572,405 / 88.26%
Intronic: 7,628,894 / 7.96%
Intergenic: 3,624,562 / 3.78%
Intronic/intergenic overlapping exon: 4,306,595 / 4.49%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.19
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 31,040,815
ACCT 5.4%
AGGT 5.04%
AGGA 3.55%
ATCT 3.53%
TCCT 3.44%
GCCT 3.22%
AGCT 2.68%
CCCT 2.57%
AGGC 2.44%
TTCT 2.3%
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