Input data and parameters 

Input

Analysis date: Tue Oct 31 09:39:14 GMT 2023
BAM file: SRX7354359.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): 44,654,380 / 44,433,459
Number of aligned pairs (without duplicates): 44,410,937
Total number of alignments: 96,690,976
Number of secondary alignments: 7,603,137
Number of non-unique alignments: 12,722,812
Aligned to genes: 74,831,669
Ambiguous alignments: 325,029
No feature assigned: 8,303,413
Missing chromosome in annotation: 508,053
Not aligned: 7,746,249

Reads genomic origin

Exonic: 74,831,669 / 90.01%
Intronic: 4,667,738 / 5.61%
Intergenic: 3,635,675 / 4.37%
Intronic/intergenic overlapping exon: 3,380,284 / 4.07%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.25
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 24,445,889
ACCT 5.09%
AGGT 4.54%
ATCT 4.09%
TCCT 4.06%
AGGA 3.33%
GCCT 3.29%
CCCT 2.93%
AGCT 2.55%
AGGC 2.27%
TTCT 2.07%
AGAA 1.81%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis