Input data and parameters 

Input

Analysis date: Tue Oct 31 09:22:34 GMT 2023
BAM file: SRX7354298.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): 44,751,398 / 44,657,302
Number of aligned pairs (without duplicates): 44,641,371
Total number of alignments: 108,284,313
Number of secondary alignments: 18,875,613
Number of non-unique alignments: 17,339,374
Aligned to genes: 63,286,447
Ambiguous alignments: 233,614
No feature assigned: 19,445,592
Missing chromosome in annotation: 7,979,286
Not aligned: 15,271,464

Reads genomic origin

Exonic: 63,286,447 / 76.5%
Intronic: 10,538,203 / 12.74%
Intergenic: 8,907,389 / 10.77%
Intronic/intergenic overlapping exon: 4,041,550 / 4.89%

Transcript coverage profile

5' bias: 0.46
3' bias: 0.19
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 27,861,612
ACCT 5.21%
AGGT 4.51%
GCCT 3.52%
ATCT 3.42%
AGGA 3.33%
TCCT 3.33%
AGCT 2.78%
CCCT 2.51%
TTCT 2.37%
AGGC 2.35%
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