Input data and parameters 

Input

Analysis date: Tue Oct 31 09:47:59 GMT 2023
BAM file: SRX7354376.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): 29,692,001 / 29,673,584
Number of aligned pairs (without duplicates): 29,669,824
Total number of alignments: 63,383,786
Number of secondary alignments: 4,018,201
Number of non-unique alignments: 6,524,804
Aligned to genes: 51,186,047
Ambiguous alignments: 178,441
No feature assigned: 5,140,704
Missing chromosome in annotation: 353,790
Not aligned: 2,349,751

Reads genomic origin

Exonic: 51,186,047 / 90.87%
Intronic: 2,632,893 / 4.67%
Intergenic: 2,507,811 / 4.45%
Intronic/intergenic overlapping exon: 1,960,160 / 3.48%

Transcript coverage profile

5' bias: 0.18
3' bias: 0.16
5'-3' bias: 2.12

Junction analysis

Reads at junctions: 14,191,689
ACCT 5.43%
AGGT 4.68%
ATCT 4.21%
TCCT 4.14%
AGGA 3.22%
GCCT 2.89%
CCCT 2.83%
TTCT 2.32%
AGGC 2.25%
AGCT 2.14%
AGAA 1.87%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis