Input data and parameters 

Input

Analysis date: Mon Oct 30 20:31:18 GMT 2023
BAM file: SRX7354184.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): 46,340,904 / 46,317,068
Number of aligned pairs (without duplicates): 46,309,534
Total number of alignments: 100,184,925
Number of secondary alignments: 7,526,953
Number of non-unique alignments: 11,602,696
Aligned to genes: 79,715,103
Ambiguous alignments: 360,075
No feature assigned: 7,612,390
Missing chromosome in annotation: 894,661
Not aligned: 3,279,928

Reads genomic origin

Exonic: 79,715,103 / 91.28%
Intronic: 4,113,998 / 4.71%
Intergenic: 3,498,392 / 4.01%
Intronic/intergenic overlapping exon: 3,713,368 / 4.25%

Transcript coverage profile

5' bias: 0.13
3' bias: 0.12
5'-3' bias: 2.33

Junction analysis

Reads at junctions: 27,180,805
ACCT 5.3%
AGGT 4.67%
ATCT 4.52%
TCCT 4.24%
CCCT 3.34%
AGGA 2.73%
AGGC 2.69%
AGAC 2.39%
GCCT 2.34%
AGCT 2.02%
TTCT 1.9%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis