Input data and parameters 

Input

Analysis date: Mon Oct 30 20:44:23 GMT 2023
BAM file: SRX7354240.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): 69,451,997 / 69,319,447
Number of aligned pairs (without duplicates): 69,309,176
Total number of alignments: 146,825,075
Number of secondary alignments: 8,053,631
Number of non-unique alignments: 12,740,779
Aligned to genes: 112,059,113
Ambiguous alignments: 432,309
No feature assigned: 20,739,164
Missing chromosome in annotation: 853,710
Not aligned: 15,621,688

Reads genomic origin

Exonic: 112,059,113 / 84.38%
Intronic: 14,482,353 / 10.91%
Intergenic: 6,256,811 / 4.71%
Intronic/intergenic overlapping exon: 5,657,534 / 4.26%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.29
5'-3' bias: 1.67

Junction analysis

Reads at junctions: 47,595,351
ACCT 5.25%
AGGT 4.7%
TCCT 3.52%
GCCT 3.48%
ATCT 3.44%
AGGA 3.32%
AGCT 2.82%
CCCT 2.62%
AGGC 2.46%
TTCT 2.2%
AGAT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis