Input data and parameters 

Input

Analysis date: Sun Oct 29 12:52:31 GMT 2023
BAM file: SRX7354163.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): 43,943,341 / 43,912,079
Number of aligned pairs (without duplicates): 43,908,556
Total number of alignments: 94,359,579
Number of secondary alignments: 6,504,159
Number of non-unique alignments: 10,156,518
Aligned to genes: 72,638,903
Ambiguous alignments: 235,389
No feature assigned: 10,570,707
Missing chromosome in annotation: 758,062
Not aligned: 2,723,408

Reads genomic origin

Exonic: 72,638,903 / 87.3%
Intronic: 6,723,580 / 8.08%
Intergenic: 3,847,127 / 4.62%
Intronic/intergenic overlapping exon: 2,866,888 / 3.45%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.2
5'-3' bias: 1.79

Junction analysis

Reads at junctions: 21,157,869
ACCT 5.38%
AGGT 4.54%
ATCT 3.57%
TCCT 3.43%
GCCT 3.41%
AGGA 3.4%
AGCT 2.72%
CCCT 2.47%
AGGC 2.42%
TTCT 2.36%
AGAT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis