Input data and parameters 

Input

Analysis date: Mon Oct 30 22:12:58 GMT 2023
BAM file: SRX7354244.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): 18,291,837 / 18,281,733
Number of aligned pairs (without duplicates): 18,280,040
Total number of alignments: 38,943,229
Number of secondary alignments: 2,369,659
Number of non-unique alignments: 3,890,389
Aligned to genes: 30,311,160
Ambiguous alignments: 110,610
No feature assigned: 4,449,287
Missing chromosome in annotation: 181,783
Not aligned: 1,687,854

Reads genomic origin

Exonic: 30,311,160 / 87.2%
Intronic: 3,104,436 / 8.93%
Intergenic: 1,344,851 / 3.87%
Intronic/intergenic overlapping exon: 1,164,664 / 3.35%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.19
5'-3' bias: 2.2

Junction analysis

Reads at junctions: 10,310,923
ACCT 5.27%
AGGT 4.7%
TCCT 3.61%
ATCT 3.56%
AGGA 3.55%
GCCT 2.94%
AGCT 2.7%
CCCT 2.45%
AGGC 2.41%
AGAT 2.23%
TTCT 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